July 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2479: Performance improvements for large histories (...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3f407d489ade changeset: 2479:3f407d489ade user: James Taylor <james(a)jamestaylor.org> date: Fri May 22 14:46:17 2009 -0400 description: Performance improvements for large histories (both on database query and javascript) 5 file(s) affected in this change: lib/galaxy/datatypes/registry.py lib/galaxy/model/mapping.py lib/galaxy/web/controllers/root.py lib/galaxy/web/framework/__init__.py templates/root/history.mako diffs (243 lines): diff -r feb7438276fb -r 3f407d489ade lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri May 22 14:46:17 2009 -0400 @@ -211,7 +211,8 @@ builder = self.datatypes_by_extension[ext] except KeyError: builder = data.Text() - self.log.warning('unknown extension in data factory %s' % ext) + if ext is not None: + self.log.warning('unknown extension in data factory %s', ext) return builder def change_datatype(self, data, ext ): diff -r feb7438276fb -r 3f407d489ade lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/model/mapping.py Fri May 22 14:46:17 2009 -0400 @@ -690,7 +690,7 @@ assign_mapper( context, History, History.table, properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), - active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ) + active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), viewonly=True ) ) ) assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation.table, diff -r feb7438276fb -r 3f407d489ade lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri May 22 14:46:17 2009 -0400 @@ -61,7 +61,18 @@ return trans.fill_template_mako( "root/history_as_xml.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) ) else: template = "root/history.mako" - return trans.fill_template( "root/history.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) ) + show_deleted = util.string_as_bool( show_deleted ) + query = trans.sa_session.query( model.HistoryDatasetAssociation ) \ + .filter( model.HistoryDatasetAssociation.history == history ) \ + .options( eagerload( "children" ) ) \ + .join( "dataset" ).filter( model.Dataset.purged == False ) \ + .options( eagerload_all( "dataset.actions" ) ) + if not show_deleted: + query.filter_by( deleted=False ) + return trans.stream_template_mako( "root/history.mako", + history = history, + datasets = query.all(), + show_deleted = show_deleted ) @web.expose def dataset_state ( self, trans, id=None, stamp=None ): diff -r feb7438276fb -r 3f407d489ade lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri May 22 14:46:17 2009 -0400 @@ -23,6 +23,7 @@ pkg_resources.require( "Mako" ) import mako.template import mako.lookup +import mako.runtime pkg_resources.require( "Babel" ) from babel.support import Translations @@ -575,6 +576,23 @@ data.update( self.template_context ) data.update( kwargs ) return template.render( **data ) + def stream_template_mako( self, filename, **kwargs ): + template = self.webapp.mako_template_lookup.get_template( filename ) + template.output_encoding = 'utf-8' + data = dict( caller=self, t=self, trans=self, h=webhelpers, util=util, request=self.request, response=self.response, app=self.app ) + data.update( self.template_context ) + data.update( kwargs ) + ## return template.render( **data ) + def render( environ, start_response ): + response_write = start_response( self.response.wsgi_status(), + self.response.wsgi_headeritems() ) + class C: + def write( self, *args, **kwargs ): + response_write( *args, **kwargs ) + context = mako.runtime.Context( C(), **data ) + template.render_context( context ) + return [] + return render def fill_template_string(self, template_string, context=None, **kwargs): """ Fill in a template, putting any keyword arguments on the context. diff -r feb7438276fb -r 3f407d489ade templates/root/history.mako --- a/templates/root/history.mako Mon Jul 13 13:08:52 2009 -0400 +++ b/templates/root/history.mako Fri May 22 14:46:17 2009 -0400 @@ -70,7 +70,15 @@ $("#history-name-area").append( t ); t.focus(); return false; - }) + }); + // Updater + updater({ + %for data in reversed( datasets ): + %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: + "${data.id}": "${data.state}"; + %endif + %endfor + }); }) //' Functionized so AJAX'd datasets can call them // Get shown/hidden state from cookie @@ -80,7 +88,7 @@ var state = new CookieSet( "galaxy.history.expand_state" ); for ( id in state.store ) { if ( id ) { - $( "#" + id ).children( "div.historyItemBody" ).show(); + $( "#" + id + " div.historyItemBody" ).show(); } } // If Mozilla, hide scrollbars in hidden items since they cause animation bugs @@ -114,51 +122,51 @@ state.add( id ); state.save(); delete state; } - return false; + return false; }); // Delete link $(this).find( "a.historyItemDelete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#progress-' + data_id ).show(); - $.ajax({ - url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Delete failed" ) }, - success: function() { - %if show_deleted: - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - %else: - $( "#historyItem-" + data_id ).fadeOut( "fast", function() { - $( "#historyItemContainer-" + data_id ).remove(); - if ( $( "div.historyItemContainer" ).length < 1 ) { - $( "#emptyHistoryMessage" ).show(); - } + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#progress-' + data_id ).show(); + $.ajax({ + url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Delete failed" ) }, + success: function() { + %if show_deleted: + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + %else: + $( "#historyItem-" + data_id ).fadeOut( "fast", function() { + $( "#historyItemContainer-" + data_id ).remove(); + if ( $( "div.historyItemContainer" ).length < 1 ) { + $( "#emptyHistoryMessage" ).show(); + } + }); + %endif + } + }); + return false; }); - %endif - } }); - return false; - }); - }); // Undelete link $(this).find( "a.historyItemUndelete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#progress-' + data_id ).show(); - $.ajax({ - url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Undelete failed" ) }, - success: function() { - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - } + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#progress-' + data_id ).show(); + $.ajax({ + url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Undelete failed" ) }, + success: function() { + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + } + }); + return false; + }); }); - return false; - }); - }); }); }; // Looks for changes in dataset state using an async request. Keeps @@ -261,36 +269,21 @@ <%namespace file="history_common.mako" import="render_dataset" /> -<% activatable_datasets = history.activatable_datasets %> +%if not datasets: -%if ( show_deleted and not activatable_datasets ) or ( not show_deleted and not history.active_datasets ): <div class="infomessagesmall" id="emptyHistoryMessage"> + %else: - <% - if show_deleted: - ## All datasets - datasets_to_show = activatable_datasets - else: - ## Active (not deleted) - datasets_to_show = history.active_datasets - %> + ## Render requested datasets, ordered from newest to oldest - %for data in reversed( datasets_to_show ): + %for data in reversed( datasets ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted )} </div> %endif %endfor - <script type="text/javascript"> - var tracked_datasets = {}; - %for data in reversed( history.active_datasets ): - %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: - tracked_datasets[ ${data.id} ] = "${data.state}"; - %endif - %endfor - updater( tracked_datasets ); - </script> + <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> %endif ${_("Your history is empty. Click 'Get Data' on the left pane to start")}

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[hg] galaxy 2478: Pre-compressing CSS with yui-compressor
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/feb7438276fb changeset: 2478:feb7438276fb user: James Taylor <james(a)jamestaylor.org> date: Mon Jul 13 13:08:52 2009 -0400 description: Pre-compressing CSS with yui-compressor 10 file(s) affected in this change: static/june_2007_style/blue/base.css static/june_2007_style/blue/history.css static/june_2007_style/blue/iphone.css static/june_2007_style/blue/library.css static/june_2007_style/blue/masthead.css static/june_2007_style/blue/panel_layout.css static/june_2007_style/blue/reset.css static/june_2007_style/blue/tool_menu.css static/june_2007_style/make_style.py static/june_2007_style/panel_layout.css.tmpl diffs (1871 lines): diff -r d202e2f4b910 -r feb7438276fb static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Jul 10 18:33:36 2009 -0400 +++ b/static/june_2007_style/blue/base.css Mon Jul 13 13:08:52 2009 -0400 @@ -1,645 +1,1 @@ -@import url( "reset.css" ); - -body -{ - font: 75% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif; - background: #FFFFFF; - color: #303030; - background-image: url(base_bg.png); - background-repeat: repeat-x; - background-position: top; - margin: 10px; -} - -img -{ - border: 0; -} - - -a:link, a:visited, a:active -{ - color: #303030; -} - -h1, h2, h3, h4 -{ - color: #023858; - /*text-shadow: #bbb 2px 2px 1px;*/ -} - -hr -{ - border: none; - height: 0px; - border-bottom: dotted #303030 1px; -} - -div.toolForm -{ - border: solid #d8b365 1px; -} - -div.toolFormTitle -{ - font-weight: bold; - padding: 5px; - padding-left: 10px; - padding-right: 10px; - background: #d2c099; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid #d8b365 1px; -} - -div.toolParamHelp -{ - color: #666; -} - -div.toolParamHelp a -{ - color: #666; -} - -div.toolFormBody -{ - background: #FFFFFF; - background-image: url(form_body_bg.png); - background-repeat: repeat-x; - background-position: top; - padding: 5px 0; -} - -div.toolFormBody div.toolFormTitle -{ - background: transparent; - border: none; - font-weight: bold; - border-bottom: solid #d8b365 1px; - margin-bottom: 5px; -} - -div.toolFormDisabled div.toolFormTitle { - background: #eee; - border-color: #999; -} - -div.toolFormDisabled { - border-color: #999; -} - -div.toolHelp -{ -} - -div.toolHelpBody -{ - width: 100%; - overflow: auto; -} - -div.titleRow { - font-weight: bold; - border-bottom: dotted gray 1px; - margin-bottom: 0.5em; - padding-bottom: 0.25em; -} - -/* Forms */ - -div.form -{ - border: solid #d8b365 1px; -} - -div.form-title -{ - font-weight: bold; - padding: 5px 10px; - background: #d2c099; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid #d8b365 1px; -} - -div.form-body -{ - padding: 5px 0; -} - -div.form-row -{ - padding: 5px 10px; -} - -div.form-title-row -{ - padding: 5px 10px; -} - -div.repeat-group-item -{ - border-left: solid #d8b365 5px; - margin-left: 10px; - margin-bottom: 10px; -} - -div.form-row-error -{ - background: #FFCCCC; -} - -div.form-row label -{ - font-weight: bold; - display: block; - margin-bottom: .2em; -} - -div.form-row-input -{ - float: left; - width: 300px; -} - -div.form-row-input > input -{ - max-width: 300px; -} - -div.form-row-error-message -{ - width: 300px; - float: left; - color: red; - font-weight: bold; - padding: 3px 0 0 1em; -} - -select, input, textarea -{ - font: inherit; - font-size: 115%; -} - -select, textarea, input[type="text"], input[type="file"], input[type="password"] -{ - -webkit-box-sizing: border-box; - max-width: 300px; -} - -/* Messages */ - -.errormessage, .warningmessage, .donemessage, .infomessage, .welcomeBlue, .welcomeRed , .screencastBox, .yellowbox, .redbox, .bluebox, .greenbox -{ - padding: 10px; - padding-left: 52px; - min-height: 32px; - border: 1px solid #AA6666; - background-color: #FFCCCC; - background-image: url(error_message_icon.png); - background-repeat: no-repeat; - background-position: 10px 10px; -} - -.warningmessage -{ - background-image: url(warn_message_icon.png); - border-color: #AAAA66; - background-color: #FFFFCC; -} - -.donemessage -{ - background-image: url(done_message_icon.png); - border-color: #66AA66; - background-color: #CCFFCC; -} - -.infomessage -{ - background-image: url(info_message_icon.png); - border-color: #6666AA; - background-color: #CCCCFF; -} - -.welcomeBlue -{ - padding-left: 10px; - border-color: #6666AA; - background-color: #CCCCFF; - background-image: none; -} - -.welcomeRed -{ - padding-left: 10px; - border-color: #AA6666; - background-color: #FFCCCC; - background-image: none; -} - -.screencastBox -{ - padding-left: 10px; - border-color: #AAAA66; - background-color: #FFFFCC; - background-image: none; -} - -.redbox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #FF6666; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - min-height: 32px; - -} - -.yellowbox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #FFCC00; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - min-height: 32px; -} - -.bluebox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #6666FF; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - color: #FFFFFF; - min-height: 32px; -} - -.greenbox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #00CC00; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - min-height: 32px; -} - -.redbox li, .yellowbox li, .bluebox li, .greenbox li { - list-style: disc; - text-transform: none; - list-style-position: inside; - list-style-image: none; - margin: 3px; -} - - -.errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall -{ - padding: 5px; - padding-left: 25px; - min-height: 25px; - border: 1px solid #AA6666; - background-color: #FFCCCC; - background-image: url(error_small.png); - background-repeat: no-repeat; - background-position: 5px 5px; -} - -.warningmessagesmall -{ - background-image: url(warn_small.png); - border-color: #AAAA66; - background-color: #FFFFCC; -} - -.donemessagesmall -{ - background-image: url(ok_small.png); - border-color: #66AA66; - background-color: #CCFFCC; -} - -.infomessagesmall -{ - background-image: url(info_small.png); - border-color: #6666AA; - background-color: #CCCCFF; -} - -.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr -{ - padding-left: 20px; - min-height: 15px; - background: url(error_small.png) no-repeat; -} - -.warningmark -{ - background-image: url(warn_small.png); -} - -.donemark -{ - background-image: url(ok_small.png); -} - -.infomark, .ok_bgr -{ - background-image: url(info_small.png); -} - -table.colored -{ - border-top: solid #d8b365 1px; - border-bottom: solid #d8b365 1px; -} - -table.colored td, table.colored th -{ - text-align: left; - padding: 5px; -} - -table.colored tr.header -{ - background: #ebd9b2; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid #d8b365 1px; - font-weight: bold; -} - -table.colored tr -{ - background: white; -} - -table.colored tr.odd_row -{ - background: #DADFEF; -} - -div.debug -{ - margin: 10px; - padding: 5px; - background: #FFFF99; - border: solid #FFFF33 1px; - color: black; -} - -div.odd_row -{ - background: #DADFEF; -} - -#footer { - display: none; -} - - -td.panel-body -{ - background: white; - color: #303030; - background: #C1C9E5 url(menu_bg.png) top repeat-x; -} - -div.toolSectionPad -{ - margin: 0; - padding: 0; - height: 5px; - font-size: 0px; -} - -div.toolSectionDetailsInner -{ - margin-left: 5px; - margin-right: 5px; -} - -div.toolSectionTitle -{ - padding-bottom: 0px; - font-weight: bold; -} - -div.toolTitle -{ - padding-top: 5px; - padding-bottom: 5px; - margin-left: 16px; - margin-right: 10px; - display: list-item; - list-style: square outside; -} - -span.toolParameterExpandableCollapsable -{ - font-weight: bold; - cursor: pointer; -} -ul.toolParameterExpandableCollapsable -{ - list-style: none; -} - -ul.manage-table-actions { - float: right; - margin-top: -2.5em; -} -ul.manage-table-actions li { - display: block; - float: left; - margin-left: 0.5em; -} - - -.state-color-queued { - border-color: #888888; - background: #EEEEEE; -} - -.state-color-ok { - border-color: #66AA66; - background: #CCFFCC; -} - -.state-color-error { - border-color: #AA6666; - background: #FFCCCC; -} - -.state-color-running { - border-color: #AAAA66; - background: #FFFFCC; -} - -.state-fg-queued { - color: #888888; -} -.state-fg-ok { - color: #66AA66; -} -.state-fg-running { - color: #AAAA66; -} -.state-fg-error { - color: #AA6666; -} - - -.action-button { - background: #eeeeee; - color: #333; - text-decoration: none; - font-size: 95%; - font-weight: bold; - display: inline-block; - cursor: pointer; - padding: 2px; - border: solid #aaaaaa 1px; - padding-right: 0.5em; - padding-left: 0.5em; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; -} - -.action-button > * { - vertical-align: middle; -} - -.action-button:hover { - color: black; - background: #dddddd; -} -.action-button:active { - color: white; - background: #aaaaaa; -} - - -div.popupmenu { - display: none; - background: #eeeeee; - color: #333; - font-size: 110%; - font-weight: bold; - font-style: normal; - white-space: nowrap; - position: absolute; - z-index: 20000; - border: solid #aaaaaa 1px; - padding: 3px 0; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; -} - -div.popupmenu-item { - padding: 3px 1em; - cursor: pointer; -} - -div.popupmenu-item:hover { - background: #aaaaaa; -} - -.popup-arrow { - font-size: 80%; - cursor: pointer; - text-decoration: none; - color: #555 -} - -.popup-arrow:hover { - color: black; -} - -div.permissionContainer { - padding-left: 20px; -} - - -.grid-header { - padding-bottom: 1em; -} - -.grid-header h2 { - margin: 0; - margin-bottom: 0.5em; -} - -.grid-header .title { - font-weight: bold; -} - -.grid { - padding-top: 1em; - border-collapse: collapse; - width: 100%; -} -.grid tbody td { - border-top: solid #DDDDDD 1px; - border-bottom: solid #DDDDDD 1px; - padding: 0.5em 1em; -} -.grid tbody td:empty { - padding: 0; -} -.grid thead th { - background: #ebd9b2; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-top: solid #d8b365 1px; - border-bottom: solid #d8b365 1px; - padding: 0.5em 1em; - text-align: left; -} -.grid tfoot td { - background-color: #F8F8F8; - border-top: solid #DDDDDD 1px; - border-bottom: solid #DDDDDD 1px; - padding: 0.5em 1em; -} -.grid .current { - background-color: #EEEEFF; -} \ No newline at end of file +@import url("reset.css");body{font:75% verdana,"Bitstream Vera Sans",geneva,arial,helvetica,helve,sans-serif;background:#FFF;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;}img{border:0;}a:link,a:visited,a:active{color:#303030;}h1,h2,h3,h4{color:#023858;}hr{border:none;height:0;border-bottom:dotted #303030 1px;}div.toolForm{border:solid #d8b365 1px;}div.toolFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#d2c099;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;}div.toolParamHelp{color:#666;}div.toolParamHelp a{color:#666;}div.toolFormBody{background:#FFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;}div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;}div.tool FormDisabled div.toolFormTitle{background:#eee;border-color:#999;}div.toolFormDisabled{border-color:#999;}div.toolHelpBody{width:100%;overflow:auto;}div.titleRow{font-weight:bold;border-bottom:dotted gray 1px;margin-bottom:.5em;padding-bottom:.25em;}div.form{border:solid #d8b365 1px;}div.form-title{font-weight:bold;padding:5px 10px;background:#d2c099;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;}div.form-body{padding:5px 0;}div.form-row{padding:5px 10px;}div.form-title-row{padding:5px 10px;}div.repeat-group-item{border-left:solid #d8b365 5px;margin-left:10px;margin-bottom:10px;}div.form-row-error{background:#FCC;}div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;}div.form-row-input{float:left;width:300px;}div.form-row-input>input{max-width:300px;}div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;}select,input,textarea{font:inherit;fo nt-size:115%;}select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;}.errormessage,.warningmessage,.donemessage,.infomessage,.welcomeBlue,.welcomeRed,.screencastBox,.yellowbox,.redbox,.bluebox,.greenbox{padding:10px;padding-left:52px;min-height:32px;border:1px solid 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-.toolbar > h1 { - position: absolute; - overflow: hidden; - left: 50%; - margin: 1px 0 0 -75px; - height: 45px; - font-size: 20px; - width: 150px; - font-weight: bold; - text-shadow: rgba(0, 0, 0, 0.4) 0px -1px 0; - text-align: center; - text-overflow: ellipsis; - white-space: nowrap; - color: #FFFFFF; -} - -body[orient="landscape"] > .toolbar > h1 { - margin-left: -125px; - width: 250px; -} - -body > .toolbar.masthead { - background: #2C3143 repeat-x; -} - -body > .toolbar.masthead > h1 { - left: 0; margin-left: 0; width: 100%; -} - - -.button { - position: absolute; - overflow: hidden; - top: 8px; - right: 6px; - margin: 0; - border-width: 0 5px; - padding: 0 3px; - width: auto; - height: 30px; - line-height: 30px; - font-family: inherit; - font-size: 12px; - font-weight: bold; - color: #FFFFFF; - text-shadow: rgba(0, 0, 0, 0.6) 0px -1px 0; - text-overflow: ellipsis; - text-decoration: none; - white-space: nowrap; - background: none; - -webkit-border-image: url(../iui/toolButton.png) 0 5 0 5; -} - -.blueButton { - -webkit-border-image: url(../iui/blueButton.png) 0 5 0 5; - border-width: 0 5px; -} - -.leftButton { - left: 6px; - right: auto; -} - -#backButton { - display: none; - left: 6px; - right: auto; - padding: 0; - max-width: 55px; - border-width: 0 8px 0 14px; - -webkit-border-image: url(../iui/backButton.png) 0 8 0 14; -} - -.whiteButton, -.grayButton { - display: block; - border-width: 0 12px; - padding: 10px; - text-align: center; - font-size: 20px; - font-weight: bold; - text-decoration: inherit; - color: inherit; -} - -.whiteButton { - -webkit-border-image: url(../iui/whiteButton.png) 0 12 0 12; - text-shadow: rgba(255, 255, 255, 0.7) 0 1px 0; -} - -.grayButton { - -webkit-border-image: url(../iui/grayButton.png) 0 12 0 12; - color: #FFFFFF; -} - -/************************************************************************************************/ - -body > ul > li { - position: relative; - margin: 0; - border-bottom: 1px solid #E0E0E0; - padding: 8px 0 8px 10px; - font-size: 20px; - font-weight: bold; - list-style: none; -} - -body > ul > li.group { - position: relative; - top: -1px; - margin-bottom: -2px; - border-top: 1px solid #7d7d7d; - border-bottom: 1px solid #999999; - padding: 1px 10px; - background: url(../iui/listGroup.png) repeat-x; - font-size: 17px; - font-weight: bold; - text-shadow: rgba(0, 0, 0, 0.4) 0 1px 0; - color: #FFFFFF; -} - -body > ul > li.group:first-child { - top: 0; - border-top: none; -} - -body > ul > li > a { - display: block; - margin: -8px 0 -8px -10px; - padding: 8px 32px 8px 10px; - text-decoration: none; - color: inherit; - background: url(../iui/listArrow.png) no-repeat right center; -} - -a[target="_replace"] { - box-sizing: border-box; - -webkit-box-sizing: border-box; - padding-top: 25px; - padding-bottom: 25px; - font-size: 18px; - color: cornflowerblue; - background-color: #FFFFFF; - background-image: none; -} - -/************************************************************************************************/ - -body > .dialog { - top: 0; - width: 100%; - min-height: 417px; - z-index: 2; - background: rgba(0, 0, 0, 0.8); - padding: 0; - text-align: right; -} - -.dialog > fieldset { - box-sizing: border-box; - -webkit-box-sizing: border-box; - width: 100%; - margin: 0; - border: none; - border-top: 1px solid #6d84a2; - padding: 10px 6px; - background: url(../iui/toolbar.png) #7388a5 repeat-x; -} - -.dialog > fieldset > h1 { - margin: 0 10px 0 10px; - padding: 0; - font-size: 20px; - font-weight: bold; - color: #FFFFFF; - text-shadow: rgba(0, 0, 0, 0.4) 0px -1px 0; - text-align: center; -} - -.dialog > fieldset > label { - position: absolute; - margin: 16px 0 0 6px; - font-size: 14px; - color: #999999; -} - - - -input:not(input[type|=radio]):not(input[type|=checkbox]) { - box-sizing: border-box; - -webkit-box-sizing: border-box; - width: 100%; - margin: 8px 0 0 0; - padding: 6px 6px 6px 44px; - 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b/static/june_2007_style/blue/reset.css Mon Jul 13 13:08:52 2009 -0400 @@ -1,3 +1,1 @@ -/* Copyright (c) 2008, Yahoo! Inc. All rights reserved. */ -body{font:13px/1.231 arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea{font:99% arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} -/*body,div,dl,dt,dd,ul,ol,li,h1,h2,h3,h4,h5,h6,pre,form,fieldset,input,textarea,p,blockquote,th,td{margin:0;padding:0;}table{border-collapse:collapse;border-spacing:0;}fieldset,img{border:0;}address,caption,cite,code,dfn,em,strong,th,var{font-style:normal;font-weight:normal;}ol,ul {list-style:none;}caption,th {text-align:left;}h1,h2,h3,h4,h5,h6{font-size:100%;font-weight:normal;}q:before,q:after{content:'';}abbr,acronym {border:0;}*/ +body{font:13px/1.231 arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea{font:99% arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} \ No newline at end of file diff -r d202e2f4b910 -r feb7438276fb static/june_2007_style/blue/tool_menu.css --- a/static/june_2007_style/blue/tool_menu.css Fri Jul 10 18:33:36 2009 -0400 +++ b/static/june_2007_style/blue/tool_menu.css Mon Jul 13 13:08:52 2009 -0400 @@ -1,69 +1,1 @@ -body -{ - background: white; - color: #303030; - background: #C1C9E5 url(menu_bg.png) top repeat-x; - margin: 5px; - margin-right: 10px; - margin-left: 10px; -} - -hr -{ - border: none; - height: 0px; - margin-top: 0px; -} - -div.toolSectionPad -{ - margin: 0; - padding: 0; - height: 5px; - font-size: 0px; -} - -div.toolSectionDetailsInner -{ - margin-left: 5px; - margin-right: 5px; -} - -div.toolSectionTitle -{ - font-weight: bold; -} - -div.toolPanelLabel -{ - padding-top: 10px; - padding-bottom: 5px; - font-weight: bold; - color: gray; - text-transform: uppercase; -} - -div.toolTitle -{ - padding-top: 5px; - padding-bottom: 5px; - margin-left: 16px; - margin-right: 10px; - display: list-item; - list-style: square outside; -} - -div.toolSectionBody div.toolPanelLabel -{ - padding-top: 5px; - padding-bottom: 5px; - margin-left: 16px; - margin-right: 10px; - display: list-item; - list-style: none outside; -} - -div.toolTitleNoSection -{ - padding-bottom: 0px; -} +body{background:white;color:#303030;background:#C1C9E5 url(menu_bg.png) top repeat-x;margin:5px;margin-right:10px;margin-left:10px;}hr{border:none;height:0;margin-top:0;}div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0;}div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;}div.toolSectionTitle{font-weight:bold;}div.toolPanelLabel{padding-top:10px;padding-bottom:5px;font-weight:bold;color:gray;text-transform:uppercase;}div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;}div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;}div.toolTitleNoSection{padding-bottom:0;} \ No newline at end of file diff -r d202e2f4b910 -r feb7438276fb static/june_2007_style/make_style.py --- a/static/june_2007_style/make_style.py Fri Jul 10 18:33:36 2009 -0400 +++ b/static/june_2007_style/make_style.py Mon Jul 13 13:08:52 2009 -0400 @@ -4,7 +4,7 @@ #import pkg_resources #pkg_resources.require("Cheetah") -import sys, string, os.path +import sys, string, os.path, tempfile, subprocess #from galaxy import eggs import pkg_resources pkg_resources.require( "Cheetah" ) @@ -73,7 +73,18 @@ for input, output in templates: print input ,"->", output - open( os.path.join( out_dir, output ), "w" ).write( str( Template( file=input, searchList=[context] ) ) ) + out_fname = os.path.join( out_dir, output ) + temp_file = tempfile.NamedTemporaryFile() + # Write processed template to temporary file + print "Processing template..." + temp_file.write( str( Template( file=input, searchList=[context] ) ) ) + temp_file.flush() + # Compress CSS with YUI + print "Compressing..." + subprocess.call( + "java -jar ../../scripts/yuicompressor.jar --type css %s -o %s" % ( temp_file.name, out_fname ), + shell = True ) + """ for rule, output in images: diff -r d202e2f4b910 -r feb7438276fb static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Jul 10 18:33:36 2009 -0400 +++ b/static/june_2007_style/panel_layout.css.tmpl Mon Jul 13 13:08:52 2009 -0400 @@ -1,3 +1,11 @@ +#set $unselectable = """ + user-select: none; + -moz-user-select: none; + -webkit-user-select: none; +""" + +## Rules + body, html { overflow: hidden; @@ -124,9 +132,6 @@ padding-left: 10px; color: #333; font-weight: bold; - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; } .unified-panel-header-inner { @@ -281,17 +286,14 @@ padding: 0 10px; height: 100%; white-space: nowrap; - -moz-user-select: none; - -khtml-user-select: none; - user-select: none; cursor: default; + ${unselectable} } .tab-group .tab { - background: ${masthead_bg}; + background: ${masthead_bg}; position: relative; - display: block; float: left; margin: 0; padding: 0 1em;

1 0

[hg] galaxy 2480: Fix job recovery when a tool has been removed ...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dc5068efc3e7 changeset: 2480:dc5068efc3e7 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jul 14 11:33:42 2009 -0400 description: Fix job recovery when a tool has been removed while the job is running 1 file(s) affected in this change: lib/galaxy/jobs/__init__.py diffs (24 lines): diff -r 3f407d489ade -r dc5068efc3e7 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri May 22 14:46:17 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Tue Jul 14 11:33:42 2009 -0400 @@ -119,10 +119,17 @@ """ model = self.app.model for job in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all(): - log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) - self.queue.put( ( job.id, job.tool_id ) ) + if job.tool_id not in self.app.toolbox.tools_by_id: + log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) + JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' ) + else: + log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) + self.queue.put( ( job.id, job.tool_id ) ) for job in model.Job.filter( (model.Job.c.state == model.Job.states.RUNNING) | (model.Job.c.state == model.Job.states.QUEUED) ).all(): - if job.job_runner_name is None: + if job.tool_id not in self.app.toolbox.tools_by_id: + log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) + JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' ) + elif job.job_runner_name is None: log.debug( "no runner: %s is still in queued state, adding to the jobs queue" %job.id ) self.queue.put( ( job.id, job.tool_id ) ) else:

1 0

[hg] galaxy 2475: Fix for tool frame refresh when require_login ...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0b5d64cde142 changeset: 2475:0b5d64cde142 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jul 10 16:15:32 2009 -0400 description: Fix for tool frame refresh when require_login config setting is true ( resolves ticket 100 ), eliminate center instead of end of history item name in DataToolParameter if name is > 30 chars ( resolves ticket # 64 ), and a log an error instead of raising an exception in get_history() if None is returned ( better behavior ). 3 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py lib/galaxy/web/controllers/user.py lib/galaxy/web/framework/__init__.py diffs (60 lines): diff -r 615a0bcf870b -r 0b5d64cde142 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Fri Jul 10 15:24:01 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Jul 10 16:15:32 2009 -0400 @@ -1115,6 +1115,10 @@ # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): for i, hda in enumerate( hdas ): + if len( hda.name ) > 30: + hda_name = '%s..%s' % ( hda.name[:17], hda.name[-11:] ) + else: + hda_name = hda.name if parent_hid is not None: hid = "%s.%d" % ( parent_hid, i + 1 ) else: @@ -1132,7 +1136,7 @@ continue if isinstance( hda.datatype, self.formats): selected = ( value and ( hda in value ) ) - field.add_option( "%s: %s" % ( hid, hda.name[:30] ), hda.id, selected ) + field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) if target_ext: @@ -1141,7 +1145,7 @@ if not trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=hda.dataset ): continue selected = ( value and ( hda in value ) ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda.name[:30] ), hda.id, selected ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) # Also collect children via association object dataset_collector( hda.children, hid ) dataset_collector( history.active_datasets, None ) diff -r 615a0bcf870b -r 0b5d64cde142 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Fri Jul 10 15:24:01 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Fri Jul 10 16:15:32 2009 -0400 @@ -168,8 +168,8 @@ mail = os.popen("%s -t" % trans.app.config.sendmail_path, 'w') mail.write("To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list." % (trans.app.config.mailing_join_addr,email) ) if mail.close(): - return trans.show_warn_message( "Now logged in as " + user.email+". However, subscribing to the mailing list has failed.", refresh_frames=['masthead', 'history'] ) - return trans.show_ok_message( "Now logged in as " + user.email, refresh_frames=['masthead', 'history'] ) + return trans.show_warn_message( "Now logged in as " + user.email+". However, subscribing to the mailing list has failed.", refresh_frames=refresh_frames ) + return trans.show_ok_message( "Now logged in as " + user.email, refresh_frames=refresh_frames ) return trans.show_form( web.FormBuilder( web.url_for(), "Create account", submit_text="Create" ) .add_text( "email", "Email address", value=email, error=email_error ) diff -r 615a0bcf870b -r 0b5d64cde142 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Jul 10 15:24:01 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Jul 10 16:15:32 2009 -0400 @@ -456,7 +456,9 @@ if util.string_as_bool( create ): history = self.new_history() else: - raise "get_history() returning None" + # Perhaps a bot is running a tool without having logged in to get a history + log.debug( "Error: this request returned None from get_history(): %s" % self.request.browser_url ) + return None return history def set_history( self, history ): if history and not history.deleted:

1 0

[hg] galaxy 2476: IE compatibility fixes in workflow editor java...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/14fd033f08eb changeset: 2476:14fd033f08eb user: James Taylor <james(a)jamestaylor.org> date: Fri Jul 10 16:21:19 2009 -0400 description: IE compatibility fixes in workflow editor javascript (groan) 2 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js static/scripts/packed/galaxy.workflow_editor.canvas.js diffs (474 lines): diff -r 0b5d64cde142 -r 14fd033f08eb static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Fri Jul 10 16:15:32 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Fri Jul 10 16:21:19 2009 -0400 @@ -2,7 +2,7 @@ this.element = element; this.connectors = []; } -Terminal.prototype = { +$.extend( Terminal.prototype, { connect: function ( connector ) { this.connectors.push( connector ); if ( this.node ) { @@ -25,26 +25,26 @@ c.destroy(); }); } -} +}); function OutputTerminal( element, datatype ) { Terminal.call( this, element ); this.datatype = datatype; } -OutputTerminal.prototype = new Terminal; +OutputTerminal.prototype = new Terminal(); function InputTerminal( element, datatypes ) { Terminal.call( this, element ); this.datatypes = datatypes; } -InputTerminal.prototype = new Terminal; +InputTerminal.prototype = new Terminal(); $.extend( InputTerminal.prototype, { can_accept: function ( other ) { if ( this.connectors.length < 1 ) { - for ( t in this.datatypes ) { + for ( var t in this.datatypes ) { // FIXME: No idea what to do about this case if ( other.datatype == "input" ) { return true; } if ( issubtype( other.datatype, this.datatypes[t] ) ) { @@ -60,7 +60,7 @@ this.canvas = null; this.dragging = false; this.inner_color = "#FFFFFF"; - this.outer_color = "#D8B365" + this.outer_color = "#D8B365"; if ( handle1 && handle2 ) { this.connect( handle1, handle2 ); } @@ -90,10 +90,16 @@ G_vmlCanvasManager.initElement( this.canvas ); } canvas_container.append( $(this.canvas) ); - if ( this.dragging ) { this.canvas.style.zIndex = "300" } + if ( this.dragging ) { + this.canvas.style.zIndex = "300"; + } } - var relativeLeft = function( e ) { return $(e).offset().left - canvas_container.offset().left } - var relativeTop = function( e ) { return $(e).offset().top - canvas_container.offset().top } + var relativeLeft = function( e ) { + return $(e).offset().left - canvas_container.offset().left; + }; + var relativeTop = function( e ) { + return $(e).offset().top - canvas_container.offset().top; + }; // Find the position of each handle var start_x = relativeLeft( this.handle1.element ) + 5; var start_y = relativeTop( this.handle1.element ) + 5; @@ -157,7 +163,7 @@ }).bind( "dropend", function ( e ) { e.dragProxy.terminal.connectors[0].inner_color = "#FFFFFF"; }).bind( "drop", function( e ) { - new Connector( e.dragTarget.terminal, e.dropTarget.terminal ).redraw(); + ( new Connector( e.dragTarget.terminal, e.dropTarget.terminal ) ).redraw(); }).bind( "hover", function() { // If connected, create a popup to allow disconnection if ( terminal.connectors.length > 0 ) { @@ -168,22 +174,24 @@ .append( $("<div class='buttons'></div>").append( $("<img src='../images/delete_icon.png' />").click( function() { - $.each( terminal.connectors, function( _, x ) { x.destroy() } ); + $.each( terminal.connectors, function( _, x ) { + x.destroy(); + }); t.remove(); }))) .bind( "mouseleave", function() { $(this).remove(); }); // Position it and show - t.css( { + t.css({ top: $(this).offset().top - 2, left: $(this).offset().left - t.width(), - 'padding-right': $(this).width() } - ).show(); + 'padding-right': $(this).width() + }).show(); } }); node.input_terminals[name] = terminal; - }) + }); }, enable_output_terminal : function( elements, name, type ) { var node = this; @@ -213,7 +221,7 @@ e.dragProxy.terminal.redraw(); // FIXME: global canvas_manager.update_viewport_overlay(); - } + }; onmove(); $("#canvas-container").get(0).scroll_panel.test( e, onmove ); }).bind( "dragend", function ( e ) { @@ -226,8 +234,12 @@ }); }, redraw : function () { - $.each( this.input_terminals, function( _, t ) { t.redraw() } ); - $.each( this.output_terminals, function( _, t ) { t.redraw() } ); + $.each( this.input_terminals, function( _, t ) { + t.redraw(); + }); + $.each( this.output_terminals, function( _, t ) { + t.redraw(); + }); }, destroy : function () { $.each( this.input_terminals, function( k, t ) { @@ -246,7 +258,7 @@ // Keep inactive nodes stacked from most to least recently active // by moving element to the end of parent's node list var element = this.element.get(0); - (function(p) { p.removeChild( element ); p.appendChild( element ) })(element.parentNode); + (function(p) { p.removeChild( element ); p.appendChild( element ); })(element.parentNode); // Remove active class $(element).removeClass( "toolForm-active" ); }, @@ -279,7 +291,7 @@ $.each( data.data_outputs, function( i, output ) { var t = $( "<div class='terminal output-terminal'></div>" ); node.enable_output_terminal( t, output.name, output.extension ); - var label = output.name + var label = output.name; if ( output.extension != 'input' ) { label = label + " (" + output.extension + ")"; } @@ -301,7 +313,7 @@ // Update input rows var old_body = el.find( "div.inputs" ); var new_body = $("<div class='inputs'></div>"); - var old = old_body.find( "div.input-data-row") + var old = old_body.find( "div.input-data-row"); $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); @@ -323,7 +335,7 @@ // Cleanup any leftover terminals old_body.find( "div.input-data-row > .terminal" ).each( function() { this.terminal.destroy(); - }) + }); // If active, reactivate with new form_html this.changed(); this.redraw(); @@ -344,7 +356,7 @@ function Workflow( canvas_container ) { this.canvas_container = canvas_container; this.id_counter = 0; - this.nodes = {} + this.nodes = {}; this.name = null; this.has_changes = false; } @@ -372,9 +384,9 @@ }); }, to_simple : function () { - var nodes = {} + var nodes = {}; $.each( this.nodes, function ( i, node ) { - var input_connections = {} + var input_connections = {}; $.each( node.input_terminals, function ( k, t ) { input_connections[ t.name ] = null; // There should only be 0 or 1 connectors, so this is @@ -391,10 +403,10 @@ tool_errors : node.tool_errors, input_connections : input_connections, position : $(node.element).position() - } + }; nodes[ node.id ] = node_data; - }) - return { steps: nodes } + }); + return { steps: nodes }; }, from_simple : function ( data ) { wf = this; @@ -409,7 +421,7 @@ } node.id = step.id; wf.nodes[ node.id ] = node; - max_id = Math.max( max_id, parseInt( id ) ) + max_id = Math.max( max_id, parseInt( id ) ); }); wf.id_counter = max_id + 1; // Second pass, connections @@ -423,7 +435,7 @@ node.input_terminals[ k ] ); c.redraw(); } - }) + }); }); }, clear_active_node : function() { @@ -471,31 +483,32 @@ }); }); // Assemble order, tracking levels - node_ids_by_level = [] + node_ids_by_level = []; while ( true ) { // Everything without a predecessor - level_parents = [] - $.each( n_pred, function( k, v ) { - if ( v == 0 ) { - level_parents.push( k ); + level_parents = []; + for ( var pred_k in n_pred ) { + if ( n_pred[ pred_k ] == 0 ) { + level_parents.push( pred_k ); } - }); + } if ( level_parents.length == 0 ) { break; } - node_ids_by_level.push( level_parents ) + node_ids_by_level.push( level_parents ); // Remove the parents from this level, and decrement the number // of predecessors for each successor - $.each( level_parents, function( k, v ) { + for ( var k in level_parents ) { + var v = level_parents[k]; delete n_pred[v]; - $.each( successors[v], function( sk, sv ) { - n_pred[sv] -= 1; - }); - }); + for ( var sk in successors[v] ) { + n_pred[ sucessors[v][sk] ] -= 1; + } + } } if ( n_pred.length ) { // ERROR: CYCLE! Currently we do nothing - return + return; } // Layout each level var all_nodes = this.nodes; @@ -505,7 +518,7 @@ // We keep nodes in the same order in a level to give the user // some control over ordering ids.sort( function( a, b ) { - return $(all_nodes[a].element).position().top - $(all_nodes[b].element).position().top + return $(all_nodes[a].element).position().top - $(all_nodes[b].element).position().top; }); // Position each node var max_width = 0; @@ -520,7 +533,7 @@ left += max_width + h_pad; }); // Need to redraw all connectors - $.each( all_nodes, function( _, node ) { node.redraw() } ); + $.each( all_nodes, function( _, node ) { node.redraw(); } ); }, bounds_for_all_nodes: function() { var xmin = Infinity, xmax = -Infinity, @@ -528,7 +541,7 @@ p; $.each( this.nodes, function( id, node ) { e = $(node.element); - p = e.position() + p = e.position(); xmin = Math.min( xmin, p.left ); xmax = Math.max( xmax, p.left + e.width() ); ymin = Math.min( ymin, p.top ); @@ -559,11 +572,11 @@ left: left, top: top, width: width, - height: height, + height: height }); // Move elements back if needed this.canvas_container.children().each( function() { - var p = $(this).position() + var p = $(this).position(); $(this).css( "left", p.left + xmin_delta ); $(this).css( "top", p.top + ymin_delta ); }); @@ -585,26 +598,26 @@ function prebuild_node( type, title_text, tool_id ) { var f = $("<div class='toolForm toolFormInCanvas'></div>"); var node = new Node( f ); - node.type = type + node.type = type; if ( type == 'tool' ) { node.tool_id = tool_id; } - var title = $("<div class='toolFormTitle unselectable'>" + title_text + "</div>" ) + var title = $("<div class='toolFormTitle unselectable'>" + title_text + "</div>" ); f.append( title ); f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 ); - var b = $("<div class='toolFormBody'></div>") + var b = $("<div class='toolFormBody'></div>"); var tmp = "<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>"; b.append( tmp ); node.form_html = tmp; - f.append( b ) + f.append( b ); // Fix width to computed width // Now add floats var buttons = $("<div class='buttons' style='float: right;'></div>"); buttons.append( $("<img src='../images/delete_icon.png' />").click( function( e ) { node.destroy(); } ).hover( - function() { $(this).attr( 'src', "../images/delete_icon_dark.png" ) }, - function() { $(this).attr( 'src', "../images/delete_icon.png" ) } + function() { $(this).attr( 'src', "../images/delete_icon_dark.png" ); }, + function() { $(this).attr( 'src', "../images/delete_icon.png" ); } ) ); // Place inside container f.appendTo( "#canvas-container" ); @@ -647,12 +660,12 @@ child = ext_to_type[child]; parent = ext_to_type[parent]; return ( type_to_type[child] ) && ( parent in type_to_type[child] ); -}; +} function populate_datatype_info( data ) { ext_to_type = data.ext_to_class_name; type_to_type = data.class_to_classes; -}; +} // FIXME: merge scroll panel into CanvasManager, clean up hardcoded stuff. @@ -663,14 +676,14 @@ test: function( e, onmove ) { clearTimeout( this.timeout ); var x = e.pageX, - y = e.pageY; + y = e.pageY, // Panel size and position panel = $(this.panel), panel_pos = panel.position(), panel_w = panel.width(), - panel_h = panel.height() + panel_h = panel.height(), // Viewport size and offset - viewport = panel.parent(); + viewport = panel.parent(), viewport_w = viewport.width(), viewport_h = viewport.height(), viewport_offset = viewport.offset(), @@ -747,7 +760,7 @@ top: y }); self.update_viewport_overlay(); - } + }; // Dragging within canvas background this.cc.each( function() { this.scroll_panel = new ScrollPanel( this ); @@ -766,13 +779,13 @@ }); // Dragging for overview pane this.ov.bind( "drag", function( e ) { - var in_w = self.cc.width(); - var in_h = self.cc.height() - var o_w = self.oc.width(); - var o_h = self.oc.height(); - var p = $(this).offsetParent().offset(); - var new_x_offset = e.offsetX - p.left; - var new_y_offset = e.offsetY - p.top; + var in_w = self.cc.width(), + in_h = self.cc.height(), + o_w = self.oc.width(), + o_h = self.oc.height(), + p = $(this).offsetParent().offset(), + new_x_offset = e.offsetX - p.left, + new_y_offset = e.offsetY - p.top; move( - ( new_x_offset / o_w * in_w ), - ( new_y_offset / o_h * in_h ) ); }).bind( "dragend", function() { @@ -794,15 +807,15 @@ }, update_viewport_overlay: function() { - var cc = this.cc; - var cv = this.cv; - var oc = this.oc; - var ov = this.ov; - var in_w = cc.width(); - var in_h = cc.height() - var o_w = oc.width(); - var o_h = oc.height(); - var cc_pos = cc.position() + var cc = this.cc, + cv = this.cv, + oc = this.oc, + ov = this.ov, + in_w = cc.width(), + in_h = cc.height(), + o_w = oc.width(), + o_h = oc.height(), + cc_pos = cc.position(); ov.css( { left: - ( cc_pos.left / in_w * o_w ), top: - ( cc_pos.top / in_h * o_h ), @@ -812,11 +825,11 @@ }); }, draw_overview: function() { - var canvas_el = $("#overview-canvas"); - var size = canvas_el.parent().parent().width() - var c = canvas_el.get(0).getContext("2d"); - var in_w = $("#canvas-container").width(); - var in_h = $("#canvas-container").height() + var canvas_el = $("#overview-canvas"), + size = canvas_el.parent().parent().width(), + c = canvas_el.get(0).getContext("2d"), + in_w = $("#canvas-container").width(), + in_h = $("#canvas-container").height(); var o_h, shift_h, o_w, shift_w; // Fit canvas into overview area var cv_w = this.cv.width(); @@ -853,7 +866,7 @@ c.strokeStyle = "#D8B365"; c.lineWidth = 1; $.each( workflow.nodes, function( id, node ) { - var node_element = $(node.element); + var node_element = $(node.element), position = node_element.position(), x = position.left / in_w * o_w, y = position.top / in_h * o_h, @@ -864,4 +877,4 @@ }); this.update_viewport_overlay(); } -}) \ No newline at end of file +}); \ No newline at end of file diff -r 0b5d64cde142 -r 14fd033f08eb static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri Jul 10 16:15:32 2009 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri Jul 10 16:21:19 2009 -0400 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}Terminal.prototype={connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}};function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal;function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(t in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[t])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a) }}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var o=function(c){return $(c).offset().left-d.offset().left};var j=function(c){return $(c).offset().top-d.offset().top};var i=o(this.handle1.element)+5;var g=j(this.handle1.element)+5;var q=o(this.handle2.element)+5;var n=j(this.handle2.element)+5;var f=100;var l=Math.min(i,q);var a=Math.max(i,q);var k=Math.min(g,n);var v=Math.max(g,n);var b=Math.min(Math.max(Math.abs(v-k)/2,100),300);var p=l-f;var u=k-f;var r=a-l+2*f;var m=v-k+2*f;this.canvas.style. left=p+"px";this.canvas.style.top=u+"px";this.canvas.setAttribute("width",r);this.canvas.setAttribute("height",m);i-=p;g-=u;q-=p;n-=u;var s=this.canvas.getContext("2d");s.lineCap="round";s.strokeStyle=this.outer_color;s.lineWidth=7;s.beginPath();s.moveTo(i,g);s.bezierCurveTo(i+b,g,q-b,n,q,n);s.stroke();s.strokeStyle=this.inner_color;s.lineWidth=5;s.beginPath();s.moveTo(i,g);s.bezierCurveTo(i+b,g,q-b,n,q,n);s.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){new Connector(g.dragTarget.terminal,g.dropTarget.terminal).redraw()}).bind("hover",function(){if(f. connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(j,i){i.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(l){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag", function(j){var i=function(){var l=$(j.dragProxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.dragProxy).css({left:k,top:m});j.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};i();$("#canvas-container").get(0).scroll_panel.test(j,i)}).bind("dragend",function(i){i.dragProxy.terminal.connectors[0].destroy();$(i.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a. parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);i.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<d iv class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);g.find("div[name="+j.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed( );this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,i){f[i.name]=null;$.each(i.connectors,function(j,k){f[i.name]={id:k.handle1.node.id,output _name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(i,g){if(g){var j=wf.nodes[g.id];var l=new Connector();l.connect(j.output_terminals[g.output_name],c.input_terminals[i]);l.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_form_for_tool(a.form _html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var a={};var b={};$.each(this.nodes,function(i,g){if(a[i]===undefined){a[i]=0}if(b[i]===undefined){b[i]=[]}});$.each(this.nodes,function(i,g){$.each(g.input_terminals,function(k,l){$.each(l.connectors,function(m,n){var j=n.handle1.node;a[g.id]+=1;b[j.id].push(g.id)})})});node_ids_by_level=[];while(true){level_parents=[];$.each(a,function(i,g){if(g==0){level_parents.push(i)}});if(level_parents.length==0){break}node_ids_by_level.push(level_parents);$.each(level_parents,function(i,g){delete a[g];$.each(b[g],function(k,j){a[j]-=1})})}if(a.length){return}var d=this.nodes;var c=80;v_pad=30;var f=c;$.each(node_ids_by_level,function(g,j){j.sort(function(m,i){return $(d[m].element).position().top-$(d[i].element).position().top});var k=0;var l=v_pad;$.each(j,function(i,o){var n=d[o];var m=$(n.element);$(m).css ({top:l,left:f});k=Math.max(k,$(m).width());l+=$(m).height()+v_pad});f+=k+c});$.each(d,function(g,i){i.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(i,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var j=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var i=fix_delta(a.ymin,100);d=Math.max(d,f.left);i=Math.max(i,f.top);var c=f.left-d;var g=f.top-i;var b=round_up(a.xmax+100,100)+d;var k=round_up(a.ymax+100,100)+i;b=Math.max(b,-c+j.width());k=Math.max(k,-g+j.height());this.canvas_container.css({left:c,top:g,width:b,height:k,});this.canvas_container.children().each(function(){var l=$(this).position();$(this).css("left",l.left+d);$(this).css("top",l.top+i)})}});func tion fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(m,k,s){var j=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(j);g.type=m;if(m=="tool"){g.tool_id=s}var q=$("<div class='toolFormTitle unselectable'>"+k+"</div>");j.append(q);j.css("left",$(window).scrollLeft()+20);j.css("top",$(window).scrollTop()+20);var n=$("<div class='toolFormBody'></div>");var i="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";n.append(i);g.form_html=i;j.append(n);var l=$("<div class='buttons' style='float: right;'></div>");l.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));j.appendTo("#canvas-container");var d=$("#canvas-container").position( );var c=$("#canvas-container").parent();var a=j.width();var r=j.height();j.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(r/2)});l.prependTo(q);a+=(l.width()+10);j.css("width",a);$(j).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(f,c){clearTim eout(this.timeout);var a=f.pageX,g=f.pageY;b=$(this.panel),panel_pos=b.position(),panel_w=b.width(),panel_h=b.height();viewport=b.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),viewport_offset=viewport.offset(),min_x=viewport_offset.left,min_y=viewport_offset.top,max_x=min_x+viewport.width(),max_y=min_y+viewport.height(),p_min_x=-(panel_w-(viewport_w/2)),p_min_y=-(panel_h-(viewport_h/2)),p_max_x=(viewport_w/2),p_max_y=(viewport_h/2),moved=false,close_dist=5,nudge=23;if(a-close_dist<min_x){if(panel_pos.left<p_max_x){var d=Math.min(nudge,p_max_x-panel_pos.left);b.css("left",panel_pos.left+d);moved=true}}else{if(a+close_dist>max_x){if(panel_pos.left>p_min_x){var d=Math.min(nudge,panel_pos.left-p_min_x);b.css("left",panel_pos.left-d);moved=true}}else{if(g-close_dist<min_y){if(panel_pos.top<p_max_y){var d=Math.min(nudge,p_max_y-panel_pos.top);b.css("top",panel_pos.top+d);moved=true}}else{if(g+close_dist>max_y){if(panel_pos.top>p_min_y){var d=Math.min(nudge,pane l_pos.top-p_min_x);b.css("top",(panel_pos.top-d)+"px");moved=true}}}}}if(moved){c();var b=this;this.timeout=setTimeout(function(){b.test(f,c)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var i=$(this).offset();var f=b.cc.position();c=f.top-i.top;d=f.left-i.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("dra g",function(l){var k=b.cc.width();var g=b.cc.height();var f=b.oc.width();var i=b.oc.height();var j=$(this).offsetParent().offset();var n=l.offsetX-j.left;var m=l.offsetY-j.top;a(-(n/f*k),-(m/i*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var j=$(this).offsetParent();var i=j.offset();var f=Math.max(j.width()-(g.offsetX-i.left),j.height()-(g.offsetY-i.top));$(this).css({width:f,height:f});b.draw_overview()})},update_viewport_overlay:function(){var b=this.cc;var f=this.cv;var a=this.oc;var c=this.ov;var d=b.width();var k=b.height();var j=a.width();var g=a.height();var i=b.position();c.css({left:-(i.left/d*j),top:-(i.top/k*g),width:(f.width()/d*j)-2,height:(f.height()/k*g)-2})},draw_overview:function(){var k=$("#overview-canvas");var n=k.parent().parent().width();var j=k.get(0).getContext("2d");var d=$("#canvas-container").width();var m=$("#canvas-container").height();var g,a,l,f;var i=this.cv.wi dth();var b=this.cv.height();if(d<i&&m<b){l=d/i*n;f=(n-l)/2;g=m/b*n;a=(n-g)/2}else{if(d<m){a=0;g=n;l=Math.ceil(g*d/m);f=(n-l)/2}else{l=n;f=0;g=Math.ceil(l*m/d);a=(n-g)/2}}k.parent().css({left:f,top:a,width:l,height:g});k.attr("width",l);k.attr("height",g);j.fillStyle="#D2C099";j.strokeStyle="#D8B365";j.lineWidth=1;$.each(workflow.nodes,function(p,c){var o=$(c.element);position=o.position(),x=position.left/d*l,y=position.top/m*g,w=o.width()/d*l,h=o.height()/m*g;j.fillRect(x,y,w,h);j.strokeRect(x,y,w,h)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.ha ndle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_ form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[sucessors[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$( this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prot otype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this; var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({wi dth:f,height:f});b.draw_overview()})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewp ort_overlay()}}); \ No newline at end of file

1 0

[hg] galaxy 2472: Fixed form_definition foreign key so that the ...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/249f0037dea2 changeset: 2472:249f0037dea2 user: rc date: Fri Jul 10 13:52:20 2009 -0400 description: Fixed form_definition foreign key so that the unittest will pass. Nothing needed for migration script 1 file(s) affected in this change: lib/galaxy/model/mapping.py diffs (17 lines): diff -r b46f27137744 -r 249f0037dea2 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Fri Jul 10 11:37:28 2009 -0400 +++ b/lib/galaxy/model/mapping.py Fri Jul 10 13:52:20 2009 -0400 @@ -535,7 +535,12 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), nullable=False ), Column( "desc", TEXT ), - Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True ), + Column( "form_definition_current_id", + Integer, + ForeignKey( "form_definition_current.id", + name='for_def_form_def_current_id_fk', + use_alter=True), + index=True ), Column( "fields", JSONType())) RequestType.table = Table('request_type', metadata,

1 0

[hg] galaxy 2473: Fixed a bug in form editing where some charact...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f7bdfd409b7d changeset: 2473:f7bdfd409b7d user: rc date: Fri Jul 10 14:50:17 2009 -0400 description: Fixed a bug in form editing where some characters where not appearing correctly when the form is saved. 3 file(s) affected in this change: lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/requests.py diffs (98 lines): diff -r 249f0037dea2 -r f7bdfd409b7d lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Jul 10 13:52:20 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Jul 10 14:50:17 2009 -0400 @@ -2188,10 +2188,10 @@ msg=msg, messagetype=messagetype ) def _save_request_type(self, trans, params, request_type_id): - num_states = int( params.get( 'num_states', 0 ) ) + num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) proceed = True for i in range( num_states ): - if not params.get( 'new_element_name_%i' % i, None ): + if not util.restore_text( params.get( 'new_element_name_%i' % i, None ) ): proceed = False break if not proceed: @@ -2212,8 +2212,8 @@ ss.delete() ss.flush() for i in range( num_states ): - name = params.get( 'new_element_name_%i' % i, None ) - desc = params.get( 'new_element_description_%i' % i, None ) + name = util.restore_text( params.get( 'new_element_name_%i' % i, None )) + desc = util.restore_text( params.get( 'new_element_description_%i' % i, None )) ss = trans.app.model.SampleState(name, desc, rt.id) ss.flush() msg = "The new sample type named '%s' with %s state(s) has been created" % (rt.name, num_states) diff -r 249f0037dea2 -r f7bdfd409b7d lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Fri Jul 10 13:52:20 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Fri Jul 10 14:50:17 2009 -0400 @@ -150,10 +150,10 @@ 'selectlist': '' } self.current_form['fields'].append(empty_field) def __get_field(self, params, index): - name = params.get( 'field_name_%i' % index, None ) - helptext = params.get( 'field_helptext_%i' % index, None ) - required = params.get( 'field_required_%i' % index, False ) - field_type = params.get( 'field_type_%i' % index, None ) + name = util.restore_text( params.get( 'field_name_%i' % index, None ) ) + helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) ) + required = util.restore_text( params.get( 'field_required_%i' % index, False ) ) + field_type = util.restore_text( params.get( 'field_type_%i' % index, None ) ) if field_type == 'SelectField': selectlist = self.__get_selectbox_options(params, index) else: @@ -172,7 +172,7 @@ ctr=0 sb_options = [] while True: - option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) + option = util.restore_text( params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) ) ctr = ctr+1 if option: sb_options.append(option) @@ -194,7 +194,7 @@ return None, 'Form name must be filled.' # fields for i in range( len(self.current_form['fields']) ): - if not params.get( 'field_name_%i' % i, None ): + if not util.restore_text(params.get( 'field_name_%i' % i, None )): return None, "All the field label(s) must be completed." return True, '' def __get_form(self, params): diff -r 249f0037dea2 -r f7bdfd409b7d lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Fri Jul 10 13:52:20 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Fri Jul 10 14:50:17 2009 -0400 @@ -212,12 +212,12 @@ request = trans.app.model.Request.get(request_id) form_values = trans.app.model.FormValues.get(request.form_values_id) request_form = trans.app.model.FormDefinition.get(form_values.request_form_id) - name = params.get('name', '') - desc = params.get('desc', '') - library_id = params.get('library', '') + name = util.restore_text(params.get('name', '')) + desc = util.restore_text(params.get('desc', '')) + library_id = util.restore_text(params.get('library', '')) values = {} for field in request_form.fields: - values[field['label']] = params.get(field['label'], '') + values[field['label']] = util.restore_text(params.get(field['label'], '')) if not request_id: form_values = trans.app.model.FormValues(request_form_id, values) form_values.flush() @@ -348,11 +348,11 @@ sample = trans.app.model.Sample.get(sample_id) form_data = trans.app.model.FormData.get(sample.form_data_id) form = trans.app.model.FormDefinition.get(form_data.form_definition_id) - name = params.get('name', '') - desc = params.get('desc', '') + name = util.restore_text(params.get('name', '')) + desc = util.restore_text(params.get('desc', '')) values = {} for field in sample_form.fields: - values[field['label']] = params.get(field['label'], '') + values[field['label']] = util.restore_text(params.get(field['label'], '')) if not sample_id: form_values = trans.app.model.FormValues(sample_form.id, values) form_values.flush()

1 0

[hg] galaxy 2471: First pass of the new Galaxy forms components ...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b46f27137744 changeset: 2471:b46f27137744 user: rc date: Fri Jul 10 11:37:28 2009 -0400 description: First pass of the new Galaxy forms components including requests which based on form definitions and samples. 40 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0008_galaxy_forms.py lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py lib/galaxy/web/form_builder.py lib/galaxy/web/framework/__init__.py run_functional_tests.sh templates/admin/forms/create_form.mako templates/admin/forms/edit_form.mako templates/admin/forms/manage_forms.mako templates/admin/forms/show_form_read_only.mako templates/admin/index.mako templates/admin/requests/add_states.mako templates/admin/requests/create_request_type.mako templates/admin/requests/edit_request_type.mako templates/admin/requests/grid.mako templates/admin/requests/manage_request_types.mako templates/admin/requests/view_request.mako templates/admin/samples/change_state.mako templates/admin/samples/edit_sample.mako templates/admin/samples/events.mako templates/admin/samples/grid.mako templates/admin/samples/view_sample.mako templates/base.mako templates/base_panels.mako templates/requests/grid.mako templates/requests/index.mako templates/requests/new_request.mako templates/requests/select_request_type.mako templates/requests/view_request.mako templates/sample/browse_samples.mako templates/sample/edit_sample.mako templates/sample/grid.mako templates/sample/index.mako templates/sample/new_sample.mako templates/sample/sample_events.mako templates/sample/view_sample.mako diffs (truncated from 3714 to 3000 lines): diff -r 267db48a2371 -r b46f27137744 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Jul 09 15:49:26 2009 -0400 +++ b/lib/galaxy/model/__init__.py Fri Jul 10 11:37:28 2009 -0400 @@ -14,6 +14,7 @@ import galaxy.datatypes.registry from galaxy.datatypes.metadata import MetadataCollection from galaxy.security import RBACAgent, get_permitted_actions + import logging log = logging.getLogger( __name__ ) @@ -1095,6 +1096,58 @@ raise # Return filename inside hashed directory return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) + + +class FormDefinition( object ): + def __init__(self, name=None, desc=None, fields=[], current_form_id=None): + self.name = name + self.desc = desc + self.fields = fields + self.form_definition_current_id = current_form_id + +class FormDefinitionCurrent( object ): + def __init__(self, form_definition_id=None): + self.latest_form_id = form_definition_id + +class FormValues( object ): + def __init__(self, form_def_id=None, content=None): + self.form_definition_id = form_def_id + self.content = content + +class Request( object ): + def __init__(self, name=None, desc=None, request_type_id=None, user_id=None, form_values_id=None, library_id=None): + self.name = name + self.desc = desc + self.request_type_id = request_type_id + self.form_values_id = form_values_id + self.user_id = user_id + self.library_id = library_id + +class RequestType( object ): + def __init__(self, request_form_id=None, sample_form_id=None): + self.request_form_id = request_form_id + self.sample_form_id = sample_form_id + +class Sample( object ): + def __init__(self, name=None, desc=None, request_id=None, form_values_id=None): + self.name = name + self.desc = desc + self.request_id = request_id + self.form_values_id = form_values_id + +class SampleState( object ): + def __init__(self, name=None, desc=None, request_type_id=None): + self.name = name + self.desc = desc + self.request_type_id = request_type_id + +class SampleEvent( object ): + def __init__(self, sample_id=None, sample_state_id=None, comment=''): + self.sample_id = sample_id + self.sample_state_id = sample_state_id + self.comment = comment + + ## ---- Utility methods ------------------------------------------------------- diff -r 267db48a2371 -r b46f27137744 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Jul 09 15:49:26 2009 -0400 +++ b/lib/galaxy/model/mapping.py Fri Jul 10 11:37:28 2009 -0400 @@ -520,8 +520,114 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) + +FormDefinitionCurrent.table = Table('form_definition_current', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "deleted", Boolean, index=True, default=False )) + +# new table to store all the forms which is created by the admin +FormDefinition.table = Table('form_definition', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True ), + Column( "fields", JSONType())) + +RequestType.table = Table('request_type', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) ) + +FormValues.table = Table('form_values', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "content", JSONType()) ) + +Request.table = Table('request', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), + Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + +Sample.table = Table('sample', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), + Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + +# new table to store all the possible sample states and the sample type it +# belongs to +SampleState.table = Table('sample_state', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) ) + +SampleEvent.table = Table('sample_event', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), + Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), + Column( "comment", TEXT ) ) + + + # With the tables defined we can define the mappers and setup the # relationships between the model objects. + +assign_mapper( context, Sample, Sample.table, + properties=dict( events=relation( SampleEvent, backref="sample", + order_by=desc(SampleEvent.table.c.update_time) ), + ) ) + +assign_mapper( context, FormValues, FormValues.table, properties=None) + +assign_mapper( context, Request, Request.table, properties=None) + +assign_mapper( context, RequestType, RequestType.table, + properties=dict( states=relation( SampleState, backref="request_type", + order_by=desc(SampleState.table.c.update_time) ), + ) ) + +assign_mapper( context, FormDefinition, FormDefinition.table, properties=None) + +assign_mapper( context, FormDefinitionCurrent, FormDefinitionCurrent.table, + properties=dict( forms=relation( FormDefinition, backref='form_definition_current', + cascade="all, delete-orphan", + primaryjoin=( FormDefinitionCurrent.table.c.id == FormDefinition.table.c.form_definition_current_id ) ), + latest_form=relation( FormDefinition, post_update=True, + primaryjoin=( FormDefinitionCurrent.table.c.latest_form_id == FormDefinition.table.c.id ) ) + ) ) + +assign_mapper( context, SampleEvent, SampleEvent.table, properties=None) + +assign_mapper( context, SampleState, SampleState.table, + properties=None #dict( sample=relation( Sample, backref="sample" ), + )# ) assign_mapper( context, ValidationError, ValidationError.table ) @@ -590,6 +696,8 @@ assign_mapper( context, User, User.table, properties=dict( histories=relation( History, backref="user", order_by=desc(History.table.c.update_time) ), + requests=relation( Request, backref="user", + order_by=desc(Request.table.c.update_time) ), active_histories=relation( History, primaryjoin=( ( History.table.c.user_id == User.table.c.id ) & ( not_( History.table.c.deleted ) ) ), order_by=desc( History.table.c.update_time ) ), galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ), stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user", diff -r 267db48a2371 -r b46f27137744 lib/galaxy/model/migrate/versions/0008_galaxy_forms.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,189 @@ +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) + + +FormDefinitionCurrent_table = Table('form_definition_current', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "latest_form_id", Integer, + #ForeignKey( "form_definition.id", use_alter=True, name='form_definition_current_latest_form_id_fk'), + index=True ), + Column( "deleted", Boolean, index=True, default=False )) +FormDefinition_table = Table('form_definition', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True, nullable=False ), + Column( "fields", JSONType()) ) + +FormValues_table = Table('form_values', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "content", JSONType()) ) + +RequestType_table = Table('request_type', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) ) +# request table +Request_table = Table('request', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), + Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + +Sample_table = Table('sample', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), + Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + +SampleState_table = Table('sample_state', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "desc", TEXT ), + Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) ) + +SampleEvent_table = Table('sample_event', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), + Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), + Column( "comment", TEXT ) ) + + + + +def upgrade(): + # Load existing tables + metadata.reflect() + + # Add all of the new tables above +# metadata.create_all() + try: + FormDefinitionCurrent_table.create() + except Exception, e: + log.debug( "Creating form_definition_current table failed: %s" % str( e ) ) + try: + FormDefinition_table.create() + except Exception, e: + log.debug( "Creating form_definition table failed: %s" % str( e ) ) + # Add 1 foreign key constraint to the form_definition_current table + if FormDefinitionCurrent_table and FormDefinition_table: + try: + cons = ForeignKeyConstraint( [FormDefinitionCurrent_table.c.latest_form_id], + [FormDefinition_table.c.id], + name='form_definition_current_latest_form_id_fk' ) + # Create the constraint + cons.create() + except Exception, e: + log.debug( "Adding foreign key constraint 'form_definition_current_latest_form_id_fk' to table 'form_definition_current' failed: %s" % ( str( e ) ) ) + try: + FormValues_table.create() + except Exception, e: + log.debug( "Creating form_values table failed: %s" % str( e ) ) + try: + RequestType_table.create() + except Exception, e: + log.debug( "Creating request_type table failed: %s" % str( e ) ) + try: + Request_table.create() + except Exception, e: + log.debug( "Creating request table failed: %s" % str( e ) ) + try: + Sample_table.create() + except Exception, e: + log.debug( "Creating sample table failed: %s" % str( e ) ) + try: + SampleState_table.create() + except Exception, e: + log.debug( "Creating sample_state table failed: %s" % str( e ) ) + try: + SampleEvent_table.create() + except Exception, e: + log.debug( "Creating sample_event table failed: %s" % str( e ) ) + + + +def downgrade(): + # Load existing tables + metadata.reflect() + try: + FormDefinition_table.drop() + except Exception, e: + log.debug( "Dropping form_definition table failed: %s" % str( e ) ) + try: + FormDefinitionCurrent_table.drop() + except Exception, e: + log.debug( "Dropping form_definition_current table failed: %s" % str( e ) ) + try: + FormValues_table.drop() + except Exception, e: + log.debug( "Dropping form_values table failed: %s" % str( e ) ) + try: + Request_table.drop() + except Exception, e: + log.debug( "Dropping request table failed: %s" % str( e ) ) + try: + RequestType_table.drop() + except Exception, e: + log.debug( "Dropping request_type table failed: %s" % str( e ) ) + try: + Sample_table.drop() + except Exception, e: + log.debug( "Dropping sample table failed: %s" % str( e ) ) + try: + SampleState_table.drop() + except Exception, e: + log.debug( "Dropping sample_state table failed: %s" % str( e ) ) + try: + SampleEvent_table.drop() + except Exception, e: + log.debug( "Dropping sample_event table failed: %s" % str( e ) ) + + + + diff -r 267db48a2371 -r b46f27137744 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Thu Jul 09 15:49:26 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Jul 10 11:37:28 2009 -0400 @@ -3,6 +3,7 @@ from galaxy import util, datatypes from galaxy.web.base.controller import * from galaxy.model.orm import * +import sys import logging log = logging.getLogger( __name__ ) @@ -2097,4 +2098,123 @@ else: last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype ) - + + def _get_all_forms(self, trans, all_versions=False): + ''' + This method returns all the latest forms from the + form_definition_current table if all_versions is set to True. Otherwise + this method return all the versions of all the forms from form_definition + table + ''' + if all_versions: + return trans.app.model.FormDefinition.query().all() + else: + fdc_list = trans.app.model.FormDefinitionCurrent.query().all() + return [fdc.latest_form for fdc in fdc_list] + @web.expose + @web.require_admin + def manage_request_types( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + forms = self._get_all_forms(trans, all_versions=True) + return trans.fill_template( '/admin/requests/manage_request_types.mako', + request_types=trans.app.model.RequestType.query().all(), + forms=forms, + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def request_type( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get('create', False) == 'True': + return trans.fill_template( '/admin/requests/create_request_type.mako', + forms=self._get_all_forms(trans, all_versions=False), + msg=msg, + messagetype=messagetype) + elif params.get('add_states', False) == 'True': + return trans.fill_template( '/admin/requests/add_states.mako', + sample_type_name=util.restore_text( params.name ), + desc=util.restore_text( params.description ), + num_states=int(util.restore_text( params.num_states )), + request_form_id=int(util.restore_text( params.request_form_id )), + sample_form_id=int(util.restore_text( params.sample_form_id )), + msg=msg, + messagetype=messagetype) + elif params.get('save_new', False) == 'True': + st, msg = self._save_request_type(trans, params, None) + if not st: + return trans.fill_template( '/admin/requests/create_request_type.mako', + forms=self._get_all_forms(trans, all_versions=False), + msg=msg, + messagetype='error') + return trans.fill_template( '/admin/requests/manage_request_types.mako', + request_types=trans.app.model.RequestType.query().all(), + forms=self._get_all_forms(trans, all_versions=True), + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + elif params.get('edit', False) == 'True': + rt = trans.app.model.RequestType.get(int(util.restore_text( params.id ))) + ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() + return trans.fill_template( '/admin/requests/edit_request_type.mako', + request_type=rt, + forms=self._get_all_forms(trans, all_versions=False), + states_list=ss_list, + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + elif params.get('save_changes', False) == 'True': + st = trans.app.model.SampleType.get(int(util.restore_text( params.id ))) + st, msg = self._save_sample_type(trans, params, st.id) + if st: + msg = "The sample type '%s' has been updated with the changes." % st.name + messagetype = 'done' + else: + messagetype = 'error' + ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.sample_type_id == st.id).all() + return trans.fill_template( '/admin/samples/edit_sample_type.mako', + sample_type=st, + forms=self._get_all_forms(trans, all_versions=False), + states_list=ss_list, + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + def _save_request_type(self, trans, params, request_type_id): + num_states = int( params.get( 'num_states', 0 ) ) + proceed = True + for i in range( num_states ): + if not params.get( 'new_element_name_%i' % i, None ): + proceed = False + break + if not proceed: + msg = "All the state name(s) must be completed." + return None, msg + if not request_type_id: # create a new sample type to save + rt = trans.app.model.RequestType() + else: # use the existing sample type to save changes + rt = trans.app.model.RequestType.get(request_type_id) + rt.name = util.restore_text( params.name ) + rt.desc = util.restore_text( params.description ) or "" + rt.request_form_id = int(util.restore_text( params.request_form_id )) + rt.sample_form_id = int(util.restore_text( params.sample_form_id )) + rt.flush() + # set sample states + ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() + for ss in ss_list: + ss.delete() + ss.flush() + for i in range( num_states ): + name = params.get( 'new_element_name_%i' % i, None ) + desc = params.get( 'new_element_description_%i' % i, None ) + ss = trans.app.model.SampleState(name, desc, rt.id) + ss.flush() + msg = "The new sample type named '%s' with %s state(s) has been created" % (rt.name, num_states) + return rt, msg diff -r 267db48a2371 -r b46f27137744 lib/galaxy/web/controllers/forms.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/forms.py Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,323 @@ +from galaxy.web.base.controller import * +from galaxy.model.orm import * +from galaxy.datatypes import sniff +from galaxy import util +import logging, os, sys +from galaxy.web.form_builder import * +from galaxy.tools.parameters.basic import parameter_types +from elementtree.ElementTree import XML, Element +from galaxy.util.odict import odict +import copy + +log = logging.getLogger( __name__ ) + + +class Forms( BaseController ): + @web.expose + @web.require_admin + def index( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + return trans.fill_template( "/sample/index.mako", + default_action=params.get( 'default_action', None ), + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def manage( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + return self._show_forms_list(trans, msg, messagetype) + def _show_forms_list(self, trans, msg, messagetype): + fdc_list = trans.app.model.FormDefinitionCurrent.query().all() + return trans.fill_template( '/admin/forms/manage_forms.mako', + fdc_list=fdc_list, + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + def _get_all_forms(self, trans, all_versions=False): + ''' + This method returns all the latest forms from the + form_definition_current table if all_versions is set to True. Otherwise + this method return all the versions of all the forms from form_definition + table + ''' + if all_versions: + return trans.app.model.FormDefinition.query().all() + else: + fdc_list = trans.app.model.FormDefinitionCurrent.query().all() + return [fdc.latest_form for fdc in fdc_list] + @web.expose + @web.require_admin + def new( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get('new', False) and not params.get('create_form', False): + self.current_form = {} + self.current_form['name'] = 'New Form' + self.current_form['desc'] = '' + self.current_form['fields'] = [] + inputs = [ ( 'Name', TextField('name', 40,self.current_form['name'] ) ), + ( 'Description', TextField('description', 40, self.current_form['desc']) ) ] + return trans.fill_template( '/admin/forms/create_form.mako', + inputs=inputs, + msg=msg, + messagetype=messagetype ) + elif params.get('create_form', False) == 'True': + if 'submitted' in params.new: + self.num_add_fields = 0 + fd, msg = self.__save_form(trans, params) + self.__get_saved_form(fd) + return self._show_forms_list(trans, msg, messagetype) + @web.expose + @web.require_admin + def edit( self, trans, **kwd ): + ''' + This callback method is for handling all the editing functions like: + remaning fields, adding/deleting fields, changing fields attributes + ''' + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id ))) + # SHOW THE FORM FOR EDITING. + if params.get('show_form', False) == 'True': + self.__get_saved_form(fd) + # the following two dicts store the unsaved select box options + self.del_options = {} + self.add_options = {} + return self.__show(trans, params, fd) + # DELETE FIELD + elif params.get('remove_button', False): + self.__update_current_form(params) + index = int(params.get('remove_button', None).split(' ')[2])-1 + self.__remove_field(index) + return self.__show(trans, params, fd) + # SAVE CHANGES + elif params.get('save_changes_button', False) == 'Save': + self.__update_current_form(params) + fd_new, msg = self.__save_form(trans, params, fd.form_definition_current.id) + if not fd_new: + return self.__show(trans, params, fd, msg, 'error') + else: + fd = fd_new + msg = "The form '%s' has been updated with the changes." % fd.name + return self.__show(trans, params, fd, msg) + #ADD A FIELD + elif params.get('add_field_button', False) == 'Add field': + self.__update_current_form(params) + self.__add_field() + # show the form again with one empty field + return self.__show(trans, params, fd) + # SHOW FORM READ ONLY + elif params.get('read_only', False): + return trans.fill_template( '/admin/forms/show_form_read_only.mako', + form=fd, + msg=msg, + messagetype=messagetype ) + # REFRESH PAGE, SelectField is selected/deselected as the type of a field + elif params.get('refresh', False) == 'true': + self.__update_current_form(params) + return self.__show(trans, params, fd) + # REMOVE SelectField OPTION + elif params.get('select_box_options', False) == 'remove': + #self.__update_current_form(params) + index = int(params.get( 'field_index', None )) + option = int(params.get( 'option_index', None )) + del self.current_form['fields'][index]['selectlist'][option] + return self.__show(trans, params, fd) + # ADD SelectField OPTION + elif params.get('select_box_options', False) == 'add': + #self.__update_current_form(params) + index = int(params.get( 'field_index', None )) + self.current_form['fields'][index]['selectlist'].append('') + return self.__show(trans, params, fd) + def __remove_field(self, index): + del self.current_form['fields'][index] + def __add_field(self): + ''' + add an empty field to the fields list + ''' + empty_field = { 'label': '', + 'helptext': '', + 'visible': True, + 'required': False, + 'type': BaseField.form_field_types()[0], + 'selectlist': '' } + self.current_form['fields'].append(empty_field) + def __get_field(self, params, index): + name = params.get( 'field_name_%i' % index, None ) + helptext = params.get( 'field_helptext_%i' % index, None ) + required = params.get( 'field_required_%i' % index, False ) + field_type = params.get( 'field_type_%i' % index, None ) + if field_type == 'SelectField': + selectlist = self.__get_selectbox_options(params, index) + else: + selectlist = None + return {'label': name, + 'helptext': helptext, + 'visible': True, + 'required': required, + 'type': field_type, + 'selectlist': selectlist } + def __get_selectbox_options(self, params, index): + ''' + This method gets all the options entered by the user for field when + the fieldtype is SelectField + ''' + ctr=0 + sb_options = [] + while True: + option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) + ctr = ctr+1 + if option: + sb_options.append(option) + else: + return sb_options + def __get_saved_form(self, fd): + self.current_form = {} + self.current_form['name'] = fd.name + self.current_form['desc'] = fd.desc + self.current_form['fields'] = list(copy.deepcopy(fd.fields)) + def __validate_form(self, params): + ''' + This method checks the following text inputs are filled out by the user + - the name of form + - name of all the fields + ''' + # form name + if not util.restore_text( params.name ): + return None, 'Form name must be filled.' + # fields + for i in range( len(self.current_form['fields']) ): + if not params.get( 'field_name_%i' % i, None ): + return None, "All the field label(s) must be completed." + return True, '' + def __get_form(self, params): + name = util.restore_text( params.name ) + desc = util.restore_text( params.description ) or "" + # set form fields + fields = [] + for i in range( len(self.current_form['fields']) ): + fields.append(self.__get_field(params, i)) + fields = fields + return name, desc, fields + def __update_current_form(self, params): + name, desc, fields = self.__get_form(params) + self.current_form = {} + self.current_form['name'] = name + self.current_form['desc'] = desc + self.current_form['fields'] = fields + + def __save_form(self, trans, params, fdc_id=None): + ''' + This method saves the current form + ''' + # check the form for invalid inputs + flag, msg = self.__validate_form(params) + if not flag: + return None, msg + fd = trans.app.model.FormDefinition() + fd.name, fd.desc, fd.fields = self.__get_form(params) + if fdc_id: # save changes to the existing form + # change the pointer in the form_definition_current table to point + # to this new record + fdc = trans.app.model.FormDefinitionCurrent.get(fdc_id) + else: # create a new form + fdc = trans.app.model.FormDefinitionCurrent() + # create corresponding row in the form_definition_current table + fd.form_definition_current = fdc + fdc.latest_form = fd + trans.sa_session.save_or_update( fdc ) + trans.sa_session.flush() + msg = "The new form named '%s' has been created. " % (fd.name) + request_types = trans.app.model.RequestType.query().all() + if not request_types: + msg = msg + "Now you can create requests to associate with this form." + return fd, msg + + class FieldUI(object): + def __init__(self, index, field=None, field_type=None): + ''' + This method returns a list of widgets which describes a field. This + includes label, helptext, type, & required/optional + ''' + self.index = index + self.label = TextField('field_name_'+str(index), 40, '') + self.helptext = TextField('field_helptext_'+str(index), 40, '') + self.fieldtype = SelectField('field_type_'+str(index), + refresh_on_change=True, + refresh_on_change_values=['SelectField']) + self.selectbox_options = [] + for ft in BaseField.form_field_types(): + self.fieldtype.add_option(ft, ft) + self.required = SelectField('field_required_'+str(index), display='radio') + self.required.add_option('Required', 'true') + self.required.add_option('Optional', 'true', selected=True) + if field: + self.fill(field, field_type) + def fill(self, field, field_type=None): + # label + self.label.value = field['label'] + # helptext + self.helptext.value = field['helptext'] + # type + self.fieldtype = SelectField('field_type_'+str(self.index), + refresh_on_change=True, + refresh_on_change_values=['SelectField']) + if field_type: + field['type'] = unicode(field_type) + if field_type == 'SelectField' and not field['selectlist']: + field['selectlist'] = ['', ''] + for ft in BaseField.form_field_types(): + if ft == field['type']: + self.fieldtype.add_option(ft, ft, selected=True) + if ft == 'SelectField': + self.selectbox_ui(field) + else: + self.fieldtype.add_option(ft, ft) + # required/optional + if field['required']: + self.required = SelectField('required_'+str(self.index), display='radio') + self.required.add_option('Required', 'true', selected=True) + self.required.add_option('Optional', 'true') + def selectbox_ui(self, field): + self.selectbox_options = [] + if field['selectlist']: + for ctr, option in enumerate(field['selectlist']): + self.selectbox_options.append(('Option '+str(ctr+1), + TextField('field_'+str(self.index)+'_option_'+str(ctr), + 40, option))) + def get(self): + return [( 'Label', self.label ), + ( 'Help text', self.helptext ), + ( 'Type', self.fieldtype, self.selectbox_options), + ( '', self.required)] + def __repr__(self): + return str(self.index)+'.'+self.label + def label(self): + return str(self.index)+'.'+self.label + + def __show(self, trans, params, form, msg=None, messagetype='done'): + ''' + This method displays the form and any of the changes made to it + ''' + # name & description + form_details = [ ( 'Name', TextField('name', 40, self.current_form['name']) ), + ( 'Description', TextField('description', 40, self.current_form['desc']) ) ] + # fields + field_details = [] + for index, field in enumerate(self.current_form['fields']): + field_ui = self.FieldUI(index, field) + field_details.append( field_ui.get() ) + return trans.fill_template( '/admin/forms/edit_form.mako', + form_details=form_details, + field_details=field_details, + form=form, + field_types=BaseField.form_field_types(), + msg=msg, + messagetype=messagetype ) diff -r 267db48a2371 -r b46f27137744 lib/galaxy/web/controllers/requests.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/requests.py Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,429 @@ +from galaxy.web.base.controller import * +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.model.orm import * +from galaxy.datatypes import sniff +from galaxy import util +from galaxy.util.streamball import StreamBall +import logging, tempfile, zipfile, tarfile, os, sys +from galaxy.web.form_builder import * + +log = logging.getLogger( __name__ ) + +# States for passing messages +SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + +class RequestsListGrid( grids.Grid ): + title = "Requests" + model_class = model.Request + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Name", key="name", + link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), + attach_popup=True ), + grids.GridColumn( "Description", key='desc'), + grids.GridColumn( "Sample(s)", method='number_of_samples', + link=( lambda item: iff( item.deleted, None, dict( operation="samples", id=item.id ) ) ), ), + grids.GridColumn( "Type", key="request_type_id", method='get_request_type'), + grids.GridColumn( "Last update", key="update_time", format=time_ago ) + ] + operations = [ +# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + #default_filter = dict( deleted=False ) + def get_current_item( self, trans ): + return None + def get_request_type(self, trans, request): + request_type = trans.app.model.RequestType.get(request.request_type_id) + return request_type.name + def apply_default_filter( self, trans, query ): + return query.filter_by( user=trans.user ) + def number_of_samples(self, trans, request): + return str(len(trans.app.model.Sample.filter(trans.app.model.Sample.table.c.request_id==request.id).all())) + +class SamplesListGrid( grids.Grid ): + model_class = model.Sample + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Name", key="name", + link=( lambda item: iff( item.deleted, None, dict( operation="show_sample", id=item.id ) ) ), + attach_popup=True ), + grids.GridColumn( "Description", key='desc' ), + grids.GridColumn( "Status", method="get_status", + link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )), + + grids.GridColumn( "Last update", key="update_time", format=time_ago ) + + # Valid for filtering but invisible + #grids.GridColumn( "Deleted", key="deleted", visible=False ) + ] + operations = [ +# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + + ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + def __init__(self, request): + self.request = request + def get_current_item( self, trans ): + return None + def apply_default_filter( self, trans, query ): + return query.filter_by( request_id=self.request.id ) + def get_status(self, trans, sample): + all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all() + curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id) + return curr_state.name + +class Requests( BaseController ): + request_grid = RequestsListGrid() + + @web.expose + def index( self, trans ): + return trans.fill_template( "requests/index.mako" ) + def get_authorized_libs(self, trans): + all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() + authorized_libraries = [] + for library in all_libraries: + if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library) or trans.app.security_agent.check_folder_contents(trans.user, library) or trans.app.security_agent.show_library_item(trans.user, library): + authorized_libraries.append(library) + return authorized_libraries + @web.expose + def list( self, trans, **kwargs ): + ''' + List all request made by the current user + ''' + status = message = None + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + if operation == "show_request": + id = trans.security.decode_id(kwargs['id']) + return self.show_read_only(trans, id) + elif operation == "samples": + id = trans.security.decode_id(kwargs['id']) + return self.show_samples(trans, id, kwargs) + elif operation == "show_sample": + id = trans.security.decode_id(kwargs['id']) + return self.show_sample_read_only(trans, id) + elif operation == "events": + id = trans.security.decode_id(kwargs['id']) + return self.show_events(trans, id) + # Render the list view + return self.request_grid( trans, status=status, message=message, template='/requests/grid.mako', **kwargs ) + def show_samples(self, trans, id, kwargs): + ''' + Shows all the samples associated with this request + ''' + status = message = None + request = trans.app.model.Request.get(id) + self.samples_grid = SamplesListGrid(request) + return self.samples_grid( trans, status=status, message=message, template='/sample/grid.mako', **kwargs ) + def show_read_only(self, trans, id): + ''' + Shows the request details + ''' + request = trans.app.model.Request.get(id) + request_type = trans.app.model.RequestType.get(request.request_type_id) + request_form = trans.app.model.FormDefinition.get(request_type.request_form_id) + request_values = trans.app.model.FormValues.get(request.form_values_id) + libraries = self.get_authorized_libs(trans) + # list of widgets to be rendered on the request form + request_details = [] + # main details + request_details.append(dict(label='Name', + value=request.name, + helptext='')) + request_details.append(dict(label='Description', + value=request.desc, + helptext='')) + request_details.append(dict(label='Type', + value=request_type.name, + helptext='')) + request_details.append(dict(label='Date created', + value=request.create_time, + helptext='')) + request_details.append(dict(label='Date updated', + value=request.create_time, + helptext='')) + request_details.append(dict(label='User', + value=str(trans.user.email), + helptext='')) + # library associated + request_details.append(dict(label='Library', + value=trans.app.model.Library.get(request.library_id).name, + helptext='Associated library where the resultant \ + dataset will be stored')) + # form fields + for field in request_form.fields: + if field['required']: + req = 'Required' + else: + req = 'Optional' + request_details.append(dict(label=field['label'], + value=request_values.content[field['label']], + helptext=field['helptext']+' ('+req+')')) + return trans.fill_template( '/requests/view_request.mako', + request_form_id=request_form.id, + request_details=request_details, + request_type=request_type) + @web.expose + def new(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get('select_request_type', False) == 'True': + return trans.fill_template( '/requests/select_request_type.mako', + request_types=trans.app.model.RequestType.query().all(), + libraries=self.get_authorized_libs(trans), + msg=msg, + messagetype=messagetype ) + elif params.get('create', False) == 'True': + request_type_id = int(util.restore_text( params.request_type_id )) + return self.__show_request_form(trans, params, request_type_id) + elif params.get('save', False) == 'True': + request = self.__save(trans, params) + msg = 'The new request named %s has been created' % request.name + request_type_id = int(util.restore_text( params.request_type_id )) + return trans.response.send_redirect( web.url_for( controller='requests', + action='list', + msg=msg , + messagetype='done') ) + return self.__show_request_form(trans, params, request_type_id, request=request) + def __save(self, trans, params, request_id=None): + ''' + This method save a new request if request_id is None. + ''' + if not request_id: + request_type_id = int(util.restore_text( params.request_type_id )) + request_form_id = trans.app.model.RequestType.get(request_type_id).request_form_id + request_form = trans.app.model.FormDefinition.get(request_form_id) + else: + request = trans.app.model.Request.get(request_id) + form_values = trans.app.model.FormValues.get(request.form_values_id) + request_form = trans.app.model.FormDefinition.get(form_values.request_form_id) + name = params.get('name', '') + desc = params.get('desc', '') + library_id = params.get('library', '') + values = {} + for field in request_form.fields: + values[field['label']] = params.get(field['label'], '') + if not request_id: + form_values = trans.app.model.FormValues(request_form_id, values) + form_values.flush() + request = trans.app.model.Request(name, desc, request_type_id, + trans.user.id, form_values.id, + library_id) + request.flush() + else: + form_values.content = values + form_values.flush() + return request + def __show_request_form(self, trans, params, request_type_id, request=None): + request_type = trans.app.model.RequestType.get(request_type_id) + request_form_id = request_type.request_form_id + if request: + form_values = trans.app.model.FormValues.get(request.form_values_id) + else: + form_values = None + # list of widgets to be rendered on the request form + widgets = [] + widgets.append(dict(label='Name', + widget=TextField('name'), + helptext='(Required)')) + widgets.append(dict(label='Description', + widget=TextField('desc'), + helptext='(Optional)')) + widgets[0]['widget'].set_size(40) + widgets[1]['widget'].set_size(40) + # libraries selectbox + libraries = self.get_authorized_libs(trans) + lib_list = SelectField('library') + for lib in libraries: + lib_list.add_option(lib.name, lib.id) + widgets.append(dict(label='Library', + widget=lib_list, + helptext='Associated library where the resultant \ + dataset will be stored')) + widgets = self.__create_form(trans, params, request_form_id, widgets, form_values) + title = 'Add a new request of type: %s' % request_type.name + return trans.fill_template( '/requests/new_request.mako', + request_form_id=request_form_id, + request_type=request_type, + widgets=widgets, + title=title) + + def __create_form(self, trans, params, form_id, widgets=[], form_values=None): + form = trans.app.model.FormDefinition.get(form_id) + if not form_values: + values = {} + for field in form.fields: + if field['type'] in ['SelectField' or 'CheckBoxField']: + values[field['label']] = False + else: + values[field['label']] = '' + else: + values = form_values.content + # form fields + for field in form.fields: + fw = eval(field['type'])(field['label']) + if field['type'] == 'TextField': + fw.set_size(40) + fw.value = values[field['label']] + elif field['type'] == 'TextArea': + fw.set_size(3, 40) + fw.value = values[field['label']] + elif field['type'] == 'SelectField': + for option in field['selectlist']: + fw.add_option(option, option, values[field['label']]) + elif field['type'] == 'CheckBoxField': + fw.checked = values[field['label']] + + if field['required']: + req = 'Required' + else: + req = 'Optional' + widgets.append(dict(label=field['label'], + widget=fw, + helptext=field['helptext']+' ('+req+')')) + return widgets + @web.expose + def add_sample(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + request_id = int(util.restore_text( params.get( 'id', '' ) )) + return self.__show_sample_form(trans, params, request_id) + + def __show_sample_form(self, trans, params, request_id, sample=None): + request = trans.app.model.Request.get(request_id) + request_type = trans.app.model.RequestType.get(request.request_type_id) + sample_form_id = request_type.sample_form_id + if sample: + form_values = trans.app.model.FormValues.get(sample.form_values_id) + else: + form_values = None + # list of widgets to be rendered on the request form + widgets = [] + widgets.append(dict(label='Name', + widget=TextField('name'), + helptext='(Required)')) + widgets.append(dict(label='Description', + widget=TextField('desc'), + helptext='(Optional)')) + widgets[0]['widget'].set_size(40) + widgets[1]['widget'].set_size(40) + widgets = self.__create_form(trans, params, sample_form_id, widgets, form_values) + title = 'Add a new sample to request: %s of type: %s' % (request.name, request_type.name) + return trans.fill_template( '/sample/new_sample.mako', + sample_form_id=sample_form_id, + request_id=request.id, + widgets=widgets, + title=title) + @web.expose + def samples(self, trans, **kwd): + params = util.Params( kwd ) + if params.get('save', False) == 'True': + sample = self.__save_sample(trans, params) + return trans.response.send_redirect( web.url_for( controller='requests', + action='list', + operation='samples', + id=trans.security.encode_id(sample.request_id)) ) + def __save_sample(self, trans, params, sample_id=None): + if not sample_id: + request = trans.app.model.Request.get(int(util.restore_text( params.request_id ))) + request_type = trans.app.model.RequestType.get(request.request_type_id) + sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id) + else: + sample = trans.app.model.Sample.get(sample_id) + form_data = trans.app.model.FormData.get(sample.form_data_id) + form = trans.app.model.FormDefinition.get(form_data.form_definition_id) + name = params.get('name', '') + desc = params.get('desc', '') + values = {} + for field in sample_form.fields: + values[field['label']] = params.get(field['label'], '') + if not sample_id: + form_values = trans.app.model.FormValues(sample_form.id, values) + form_values.flush() + sample = trans.app.model.Sample(name, desc, request.id, form_values.id) + sample.flush() + # set the initial state + state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request_type.id).first() + event = trans.app.model.SampleEvent(sample.id, state.id) + event.flush() + else: + form_data.content = values + form_data.flush() + return sample + def show_sample_read_only(self, trans, sample_id): + ''' + Shows the sample details + ''' + sample = trans.app.model.Sample.get(sample_id) + request = trans.app.model.Request.get(sample.request_id) + request_type = trans.app.model.RequestType.get(request.request_type_id) + sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id) + sample_values = trans.app.model.FormValues.get(sample.form_values_id) + # list of widgets to be rendered on the request form + sample_details = [] + # main details + sample_details.append(dict(label='Name', + value=sample.name, + helptext='')) + sample_details.append(dict(label='Description', + value=sample.desc, + helptext='')) + sample_details.append(dict(label='Date created', + value=sample.create_time, + helptext='')) + sample_details.append(dict(label='Date updated', + value=sample.create_time, + helptext='')) + sample_details.append(dict(label='User', + value=str(trans.user.email), + helptext='')) + sample_details.append(dict(label='Request', + value=request.name, + helptext='Name/ID of the request this sample belongs to.')) + # get the current state of the sample + all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all() + curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id) + sample_details.append(dict(label='State', + value=curr_state.name, + helptext=curr_state.desc)) + # form fields + for field in sample_form.fields: + if field['required']: + req = 'Required' + else: + req = 'Optional' + sample_details.append(dict(label=field['label'], + value=sample_values.content[field['label']], + helptext=field['helptext']+' ('+req+')')) + return trans.fill_template( '/sample/view_sample.mako', + sample_details=sample_details) + def show_events(self, trans, sample_id): + sample = trans.app.model.Sample.get(sample_id) + events_list = [] + for event in trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all(): + state = trans.app.model.SampleState.get(event.sample_state_id) + events_list.append((state.name, event.update_time, state.desc, event.comment)) + return trans.fill_template( '/sample/sample_events.mako', + events_list=events_list, + sample_name=sample.name, + request=trans.app.model.Request.get(sample.request_id).name) + + + + diff -r 267db48a2371 -r b46f27137744 lib/galaxy/web/controllers/requests_admin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,315 @@ +from galaxy.web.base.controller import * +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.model.orm import * +from galaxy.datatypes import sniff +from galaxy import util +from galaxy.util.streamball import StreamBall +import logging, tempfile, zipfile, tarfile, os, sys +from galaxy.web.form_builder import * +from datetime import datetime, timedelta + +log = logging.getLogger( __name__ ) + + +# States for passing messages +SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + +class RequestsListGrid( grids.Grid ): + title = "Requests" + model_class = model.Request + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Name", key="name", + link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), + attach_popup=True ), + grids.GridColumn( "Description", key="desc"), + grids.GridColumn( "Sample(s)", method='number_of_samples', + link=( lambda item: iff( item.deleted, None, dict( operation="samples", id=item.id ) ) ), ), + grids.GridColumn( "Type", key="request_type_id", method='get_request_type'), + grids.GridColumn( "Last update", key="update_time", format=time_ago ), + grids.GridColumn( "User", key="user_id", method='get_user') + + ] + operations = [ +# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + def get_user(self, trans, request): + return trans.app.model.User.get(request.user_id).email + def get_current_item( self, trans ): + return None + def get_request_type(self, trans, request): + request_type = trans.app.model.RequestType.get(request.request_type_id) + return request_type.name + def apply_default_filter( self, trans, query ): + return query + def number_of_samples(self, trans, request): + return str(len(trans.app.model.Sample.filter(trans.app.model.Sample.table.c.request_id==request.id).all())) + +class SamplesListGrid( grids.Grid ): + model_class = model.Sample + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Name", key="name", + link=( lambda item: iff( item.deleted, None, dict( operation="show_sample", id=item.id ) ) ), + attach_popup=True ), + grids.GridColumn( "Description", key='desc' ), + grids.GridColumn( "Status", method="get_status", + link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )), + + grids.GridColumn( "Last update", key="update_time", format=time_ago ) + + # Valid for filtering but invisible + #grids.GridColumn( "Deleted", key="deleted", visible=False ) + ] + operations = [ +# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Change state", condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), +# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + + ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + def __init__(self, request, user): + self.request = request + self.user = user + def get_current_item( self, trans ): + return None + def apply_default_filter( self, trans, query ): + return query.filter_by( request_id=self.request.id ) + def get_status(self, trans, sample): + all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all() + curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id) + return curr_state.name + +class Requests( BaseController ): + request_grid = RequestsListGrid() + + @web.expose + @web.require_admin + def index( self, trans ): + return trans.fill_template( "/admin/requests/index.mako" ) + def get_authorized_libs(self, trans): + all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() + authorized_libraries = [] + for library in all_libraries: + if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library) or trans.app.security_agent.check_folder_contents(trans.user, library) or trans.app.security_agent.show_library_item(trans.user, library): + authorized_libraries.append(library) + return authorized_libraries + @web.expose + @web.require_admin + def list( self, trans, **kwargs ): + ''' + List all request made by the current user + ''' + status = message = None + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + if operation == "show_request": + id = trans.security.decode_id(kwargs['id']) + return self.show_read_only(trans, id) + elif operation == "samples": + id = trans.security.decode_id(kwargs['id']) + return self.show_samples(trans, id, kwargs) + elif operation == "show_sample": + id = trans.security.decode_id(kwargs['id']) + return self.show_sample_read_only(trans, id) + elif operation == "change state": + id_list = [trans.security.decode_id(id) for id in util.listify(kwargs['id'])] + return self.change_state(trans, id_list) + elif operation == "events": + id = trans.security.decode_id(kwargs['id']) + return self.show_events(trans, id) + # Render the list view + return self.request_grid( trans, status=status, message=message, template='/admin/requests/grid.mako', **kwargs ) + def show_samples(self, trans, id, kwargs): + ''' + Shows all the samples associated with this request + ''' + status = message = None + request = trans.app.model.Request.get(id) + self.samples_grid = SamplesListGrid(request, trans.app.model.User.get(request.user_id)) + return self.samples_grid( trans, status=status, message=message, template='/admin/samples/grid.mako', **kwargs ) + def show_read_only(self, trans, id): + ''' + Shows the request details + ''' + request = trans.app.model.Request.get(id) + request_type = trans.app.model.RequestType.get(request.request_type_id) + request_form = trans.app.model.FormDefinition.get(request_type.request_form_id) + request_values = trans.app.model.FormValues.get(request.form_values_id) + libraries = self.get_authorized_libs(trans) + # list of widgets to be rendered on the request form + request_details = [] + # main details + request_details.append(dict(label='Name', + value=request.name, + helptext='')) + request_details.append(dict(label='Description', + value=request.desc, + helptext='')) + request_details.append(dict(label='Type', + value=request_type.name, + helptext='')) + request_details.append(dict(label='Date created', + value=request.create_time, + helptext='')) + request_details.append(dict(label='Date updated', + value=request.create_time, + helptext='')) + request_details.append(dict(label='User', + value=str(trans.user.email), + helptext='')) + # library associated + request_details.append(dict(label='Library', + value=trans.app.model.Library.get(request.library_id).name, + helptext='Associated library where the resultant \ + dataset will be stored')) + # form fields + for field in request_form.fields: + if field['required']: + req = 'Required' + else: + req = 'Optional' + request_details.append(dict(label=field['label'], + value=request_values.content[field['label']], + helptext=field['helptext']+' ('+req+')')) + return trans.fill_template( '/admin/requests/view_request.mako', + request_form_id=request_form.id, + request_details=request_details, + request_type=request_type) + + @web.expose + @web.require_admin + def samples(self, trans, **kwd): + params = util.Params( kwd ) + if params.get('save', False) == 'True': + sample = self.__save_sample(trans, params) + return self.show_samples(trans, sample.request_id, {}) + def show_sample_read_only(self, trans, sample_id): + ''' + Shows the sample details + ''' + sample = trans.app.model.Sample.get(sample_id) + request = trans.app.model.Request.get(sample.request_id) + request_type = trans.app.model.RequestType.get(request.request_type_id) + sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id) + sample_values = trans.app.model.FormValues.get(sample.form_values_id) + # list of widgets to be rendered on the request form + sample_details = [] + # main details + sample_details.append(dict(label='Name', + value=request.name, + helptext='')) + sample_details.append(dict(label='Description', + value=request.desc, + helptext='')) + sample_details.append(dict(label='Date created', + value=sample.create_time, + helptext='')) + sample_details.append(dict(label='Date updated', + value=sample.create_time, + helptext='')) + sample_details.append(dict(label='User', + value=str(trans.user.email), + helptext='')) + sample_details.append(dict(label='Request', + value=request.name, + helptext='Name/ID of the request this sample belongs to.')) + # get the current state of the sample + all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all() + curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id) + sample_details.append(dict(label='State', + value=curr_state.name, + helptext=curr_state.desc)) + # form fields + for field in sample_form.fields: + if field['required']: + req = 'Required' + else: + req = 'Optional' + sample_details.append(dict(label=field['label'], + value=sample_values.content[field['label']], + helptext=field['helptext']+' ('+req+')')) + return trans.fill_template( '/admin/samples/view_sample.mako', + sample_details=sample_details) + def __get_all_states(self, trans, sample): + request = trans.app.model.Request.get(sample.request_id) + request_type = trans.app.model.RequestType.get(request.request_type_id) + all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all() + curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id) + states_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request_type.id) + return states_list + def __get_curr_state(self, trans, sample): + all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all() + curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id) + return curr_state + def change_state(self, trans, sample_id_list): + sample = trans.app.model.Sample.get(sample_id_list[0]) + states_list = self.__get_all_states(trans, sample) + curr_state = self.__get_curr_state(trans, sample) + states_input = SelectField('select_state') + for state in states_list: + if len(sample_id_list) == 1: + if curr_state.name == state.name: + states_input.add_option(state.name+' (Current)', state.name, selected=True) + else: + states_input.add_option(state.name, state.name) + else: + states_input.add_option(state.name, state.name) + widgets = [] + widgets.append(('Select the new state of the sample(s) from the list of possible state(s)', + states_input)) + widgets.append(('Comments', TextArea('comment'))) + title = 'Change current state of sample: ' + sample.name + return trans.fill_template( '/admin/samples/change_state.mako', + widgets=widgets, title=title, + sample_id_list=util.object_to_string(sample_id_list)) + @web.expose + @web.require_admin + def save_state(self, trans, **kwd): + params = util.Params( kwd ) + sample_id_list = util.string_to_object(util.restore_text( params.sample_id_list )) + comments = util.restore_text( params.comment ) + sample = trans.app.model.Sample.get(sample_id_list[0]) + request = trans.app.model.Request.get(sample.request_id) + selected_state = util.restore_text( params.select_state ) + new_state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request.request_type_id + and trans.app.model.SampleState.table.c.name == selected_state)[0] + for sample_id in sample_id_list: + event = trans.app.model.SampleEvent(sample_id, new_state.id, comments) + event.flush() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='samples', + id=trans.security.encode_id(request.id)) ) + @web.expose + @web.require_admin + def show_events(self, trans, sample_id): + sample = trans.app.model.Sample.get(sample_id) + request = trans.app.model.Request.get(sample.request_id) + events_list = [] + for event in trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).order_by(trans.app.model.SampleEvent.c.update_time.desc()).all(): + state = trans.app.model.SampleState.get(event.sample_state_id) + delta = datetime.utcnow() - event.update_time + if delta > timedelta( minutes=60 ): + last_update = '%s hours' % int( delta.seconds / 60 / 60 ) + else: + last_update = '%s minutes' % int( delta.seconds / 60 ) + events_list.append((state.name, state.desc, last_update, event.comment)) + return trans.fill_template( '/admin/samples/events.mako', + events_list=events_list, + sample_name=sample.name, user=trans.app.model.User.get(request.user_id), + request=request.name) + \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Thu Jul 09 15:49:26 2009 -0400 +++ b/lib/galaxy/web/form_builder.py Fri Jul 10 11:37:28 2009 -0400 @@ -9,6 +9,11 @@ def get_html( self, prefix="" ): """Returns the html widget corresponding to the parameter""" raise TypeError( "Abstract Method" ) + @staticmethod + def form_field_types(): + return ['TextField', 'TextArea', 'SelectField', 'CheckboxField'] + + class TextField(BaseField): """ @@ -26,6 +31,8 @@ def get_html( self, prefix="" ): return '<input type="text" name="%s%s" size="%d" value="%s">' \ % ( prefix, self.name, self.size, self.value ) + def set_size(self, size): + self.size = int( size ) class TextArea(BaseField): """ @@ -45,6 +52,9 @@ def get_html( self, prefix="" ): return '<textarea name="%s%s" rows="%d" cols="%d">%s</textarea>' \ % ( prefix, self.name, self.rows, self.cols, self.value ) + def set_size(self, rows, cols): + self.rows = rows + self.cols = cols class CheckboxField(BaseField): """ @@ -215,6 +225,17 @@ rval.insert( 0, '<select name="%s%s"%s%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text, last_selected_value ) ) rval.append( '</select>' ) return "\n".join( rval ) + def get_selected(self): + ''' + This method returns the currently selected option's text and value + ''' + for text, value, selected in self.options: + if selected: + return text, value + if self.options: + return self.options[0] + return None + class DrillDownField( BaseField ): diff -r 267db48a2371 -r b46f27137744 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Jul 09 15:49:26 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Jul 10 11:37:28 2009 -0400 @@ -607,6 +607,11 @@ if dbkey == ds.dbkey: return ds return None + + def request_types(self): + if self.app.model.RequestType.query().all(): + return True + return False class FormBuilder( object ): """ diff -r 267db48a2371 -r b46f27137744 templates/admin/forms/create_form.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/forms/create_form.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,31 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create a new form definition</div> + <div class="toolFormBody"> + <form name="create_form" action="${h.url_for( controller='forms', action='new', create_form=True, new=False, create_fields=False )}" method="post" > + %for label, input in inputs: + <div class="form-row"> + <label>${label}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${input.get_html()} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="new" value="submitted" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <input type="submit" name="save_form" value="Save"/> + </form> + </div> +</div> diff -r 267db48a2371 -r b46f27137744 templates/admin/forms/edit_form.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/forms/edit_form.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,105 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#edit_form" ).submit(); + } + }); +}); +</script> + +<%def name="render_selectbox_options( index, field_attr )"> + %if field_attr[0] == 'Type': + %if field_attr[1].get_selected()[0] == 'SelectField': + <% options = field_attr[2] %> + <div class="repeat-group-item"> + <label> Options</label> + %for i, option in enumerate(options): + <b> ${i+1}</b> + ${option[1].get_html()} + ##<input type="submit" name="remove_option_${index}" value="Remove option ${i+1}"/><br> + <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br> + %endfor + </div> + <div class="form-row"> + <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='add', field_index=index )}">Add</a> + </div> + ##<div class="form-row"> + ## <input type="submit" name="add_option_field_${index}" value="Add option"/> + ##</div> + %endif + %endif +</%def> + + +<%def name="render_field( index, field )"> + <div class="repeat-group-item"> + <div class="form-row"> + <label>Field ${1+index}</label> + </div> + %for field_attr in field: + <div class="form-row"> + <label>${field_attr[0]}</label> + ${field_attr[1].get_html()} + ${render_selectbox_options( index, field_attr )} + </div> + %endfor + <div class="form-row"> + <input type="submit" name="remove_button" value="Remove field ${index+1}"/> + </div> + </div> +</%def> + +<div class="toolForm"> + <div class="toolFormTitle">Edit form definition '${form.name}'</div> + <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields) )}" method="post" > + %for label, input in form_details: + <div class="form-row"> + <label>${label}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${input.get_html()} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="toolFormTitle">Sample fields (${len(form.fields)})</div> + %for ctr, field in enumerate(field_details): + ${render_field( ctr, field )} + %endfor + <div class="form-row"> + <input type="submit" name="add_field_button" value="Add field"/> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <input type="submit" name="save_changes_button" value="Save"/> + </form> + </div> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/forms/manage_forms.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/forms/manage_forms.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,73 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +<%def name="title()">Manage Form Definitions</%def> + +## Render a row +<%def name="render_row( form, ctr )"> + %if ctr % 2 == 1: + <tr class="odd_row"> + %else: + <tr> + %endif + <td> + <b><a href="${h.url_for( controller='forms', action='edit', form_id=form.id, read_only=True )}">${form.name}</a></b> + <a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="form-${form.id}-popup"> + <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit form definition</a> + </div> + </td> + <td><i>${form.desc}</i></td> + </tr> +</%def> + + +<h2> + %if deleted: + Deleted + %endif + Forms +</h2> + + + +<ul class="manage-table-actions"> + %if not deleted: + <li> + <a class="action-button" href="${h.url_for( controller='forms', action='new', new=True )}"> + <img src="${h.url_for('/static/images/silk/add.png')}" /> + <span>Define a new form</span></a> + </li> + %endif +</ul> + + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if not fdc_list: + %if deleted: + There are no deleted forms + %else: + There are no forms. + %endif +%else: + <table class="grid"> + <thead> + <tr> + <th>Name</th> + <th>Description</th> + </tr> + </thead> + <tbody> + %for ctr, fdc in enumerate( fdc_list ): + <tr> + ${render_row( fdc.latest_form, ctr )} + </tr> + %endfor + </tbody> + </table> +%endif diff -r 267db48a2371 -r b46f27137744 templates/admin/forms/show_form_read_only.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/forms/show_form_read_only.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,67 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div> + <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" > + <table class = "grid"> + <tbody> + %for index, field in enumerate(form.fields): + <tr> + <td> + <div class="form-row"> + <label>${1+index}. Label</label> + <a>${field['label']}</a> + %if field['type'] == 'SelectField': + <a id="${field['label']}-popup" class="popup-arrow" style="display: none;">▼</a> + %for option in field['selectlist']: + <div popupmenu="${field['label']}-type-popup"> + <a class="action-button" href="" >${option}</a> + </div> + %endfor + %endif + </div> + </td> + <td> + <div class="form-row"> + <label>Help text </label> + %if not field['helptext']: + <a><i>No helptext</i></a> + %else: + <a>${field['helptext']}</a> + %endif + </div> + </td> + <td> + <div class="form-row"> + <label>Type:</label> + <a>${field['type']}</a> + %if field['type'] == 'SelectField': + <a id="fieldtype-popup" class="popup-arrow" style="display: none;">▼</a> + %for option in field['selectlist']: + <div popupmenu="type-popup"> + <a class="action-button" href="" >${option}</a> + </div> + %endfor + %endif + </div> + </td> + <td> + <div class="form-row"> + <label>Required?</label> + <a>${field['required']}</a> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + ##<input type="submit" name="save_changes_button" value="Back"/> + </form> + </div> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/index.mako --- a/templates/admin/index.mako Thu Jul 09 15:49:26 2009 -0400 +++ b/templates/admin/index.mako Fri Jul 10 11:37:28 2009 -0400 @@ -103,13 +103,35 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> </div> </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Forms</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a href="${h.url_for( controller='forms', action='manage' )}" target="galaxy_main">Manage forms</a></div> + </div> + </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Requests</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='manage_request_types' )}" target="galaxy_main">Manage request types</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='list')}" target="galaxy_main">Manage requests</a></div> + </div> + </div> </div> </div> </div> + ##<iframe name="galaxy_admin" src="${h.url_for( controller='admin', action='index' )}" frameborder="0" style="position: absolute; margin: 0; border: 0 none; height: 100%; width: 100%;"> </iframe> </%def> <%def name="center_panel()"> - - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( action='center' )}"> </iframe> + <% + center_url = h.url_for( action='center' ) + %> + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r 267db48a2371 -r b46f27137744 templates/admin/requests/add_states.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/add_states.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,26 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create ${num_states} states for the '${sample_type_name}' sample type</div> + <form name="new_form_fields" action="${h.url_for( controller='admin', action='request_type', save_new=True, create=False, edit=False, name=sample_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" > + <div class="toolFormBody"> + %for element_count in range( num_states ): + <div class="form-row"> + <label>${1+element_count}) State name:</label> + <input type="text" name="new_element_name_${element_count}" value="" size="40"/> + <label>State help text (optional):</label> + <input type="text" name="new_element_description_${element_count}" value="" size="40"/> + </div> + <div style="clear: both"></div> + %endfor + </div> + <div class="toolFormBody"> + <input type="submit" name="save_new_sample_type" value="Save"/> + </div> + </form> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/requests/create_request_type.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/create_request_type.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,66 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create a new request type</div> + %if not forms: + Create a form definition first to create a new request type. + %else: + <div class="toolFormBody"> + <form name="create_request_type" action="${h.url_for( controller='admin', action='request_type', add_states=True, create=False, edit=False )}" method="post" > + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="New Request Type" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="description" value="" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label> + Request Form definition: + </label> + <select name="request_form_id"> + %for form in forms: + <option value="${form.id}">${form.name}</option> + %endfor + </select> + </div> + <div class="form-row"> + <label> + Sample Form definition: + </label> + <select name="sample_form_id"> + %for form in forms: + <option value="${form.id}">${form.name}</option> + %endfor + </select> + </div> + <div class="form-row"> + <label>Number of sample states:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" size="3" name="num_states" value="1"/> + </div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="new" value="submitted" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <input type="submit" name="create_library_button" value="Define states"/> + </form> + </div> + %endif +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/requests/edit_request_type.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/edit_request_type.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,78 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<% num_states=len(states_list) %> + +<div class="toolForm"> + <div class="toolFormTitle">Edit the request type</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='request_type', save_changes=True, create=False, id=request_type.id, num_states=num_states )}" method="post" > + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${request_type.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="description" value="${request_type.desc}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label> + Request Form definition: + </label> + <select name="form_id"> + %for form in forms: + %if form.id == request_type.request_form_id: + <option value="${form.id}" selected>${form.name}</option> + %else: + <option value="${form.id}">${form.name}</option> + %endif + %endfor + </select> + </div> + <div class="form-row"> + <label> + Sample Form definition: + </label> + <select name="form_id"> + %for form in forms: + %if form.id == request_type.sample_form_id: + <option value="${form.id}" selected>${form.name}</option> + %else: + <option value="${form.id}">${form.name}</option> + %endif + %endfor + </select> + </div> + <div class="toolFormBody"> + %for element_count, state in enumerate(states_list): + <div class="form-row"> + <label>${1+element_count}) State name:</label> + <input type="text" name="new_element_name_${element_count}" value="${state.name}" size="40"/> + <label>State help text (optional):</label> + <input type="text" name="new_element_description_${element_count}" value="${state.desc}" size="40"/> + </div> + <div style="clear: both"></div> + %endfor + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="new" value="submitted" size="40"/> + </div> + <div style="clear: both"></div> + </div> + + <input type="submit" name="edit_request_type_button" value="Save"/> + </form> + </div> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/requests/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/grid.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,205 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="title()">Browse Requests</%def> + +%if message: + <p> + <div class="${message_type}message transient-message">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + </script> +</%def> + +<%def name="stylesheets()"> + <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + <style> + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + </style> +</%def> + +<div class="grid-header"> + <h2>${grid.title}</h2> + %if len(query.all()): + <h3>All Users</h3> + %endif +## %if len(query.all()): +## <span class="title">Filter:</span> +## %for i, filter in enumerate( grid.standard_filters ): +## %if i > 0: +## <span>|</span> +## %endif +## <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> +## %endfor +## %endif +</div> + + +%if not len(query.all()): + There are no request(s). +%else: +<form name="history_actions" action="${url()}" method="post" > + <table class="grid"> + <thead> + <tr> + <th></th> + %for column in grid.columns: + %if column.visible: + <% + href = "" + extra = "" + if column.sortable: + if sort_key == column.key: + if sort_order == "asc": + href = url( sort=( "-" + column.key ) ) + extra = "↓" + else: + href = url( sort=( column.key ) ) + extra = "↑" + else: + href = url( sort=column.key ) + %> + <th\ + %if column.ncells > 1: + colspan="${column.ncells}" + %endif + > + %if href: + <a href="${href}">${column.label}</a> + %else: + ${column.label} + %endif + <span>${extra}</span> + </th> + %endif + %endfor + <th></th> + </tr> + </thead> + <tbody> + %for i, item in enumerate( query ): + <tr \ + %if current_item == item: + class="current" \ + %endif + > + ## Item selection column + <td style="width: 1.5em;"> + <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> + </td> + ## Data columns + %for column in grid.columns: + %if column.visible: + <% + # Link + if column.link and column.link( item ): + href = url( **column.link( item ) ) + else: + href = None + # Value (coerced to list so we can loop) + value = column.get_value( trans, grid, item ) + if column.ncells == 1: + value = [ value ] + %> + %for cellnum, v in enumerate( value ): + <% + # Attach popup menu? + if column.attach_popup and cellnum == 0: + extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">▼</a>' % i + else: + extra = "" + %> + %if href: + <td><a href="${href}">${v}</a> ${extra}</td> + %else: + <td >${v}${extra}</td> + %endif + </td> + %endfor + %endif + %endfor + ## Actions column + <td> + <div popupmenu="grid-${i}-popup"> + %for operation in grid.operations: + %if operation.allowed( item ): + <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + %endfor + </tbody> +## <tfoot> +## <tr> +## <td></td> +## <td colspan="100"> +## For <span class="grid-selected-count"></span> selected requests: +## %for operation in grid.operations: +## %if operation.allow_multiple: +## <input type="submit" name="operation" value="${operation.label}" class="action-button"> +## %endif +## %endfor +## </td> +## </tr> +## </tfoot> + </table> +</form> +%endif \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/requests/manage_request_types.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/manage_request_types.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,60 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="title()">request Types</%def> + +<h2> + %if deleted: + Deleted + %endif + Request Types +</h2> + +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='admin', action='request_type', create=True )}"><span>Create a new request type</span></a> + </li> +</ul> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if not request_types: + %if deleted: + There are no deleted request types + %else: + There are no request types. + %endif +%else: + <table class="grid"> + <thead> + <tr> + <th>Name</th> + <th>Description</th> + <th>Request Form</th> + <th>Sample Form</th> + </tr> + </thead> + <tbody> + %for request_type in request_types: + <tr> + <td><b><a href="${h.url_for( controller='admin', action='request_type', edit='True', id=request_type.id)}">${request_type.name}</a></b></td> + <td><i>${request_type.desc}</i></td> + <% for form in forms: + if form.id == request_type.request_form_id: + form_name = form.name + break + %> + <td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.request_form_id, read_only=True)}">${form_name}</a></td> + <% for form in forms: + if form.id == request_type.sample_form_id: + form_name = form.name + break + %> + <td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.sample_form_id, read_only=True)}">${form_name}</a></td> + </tr> + %endfor + </tbody> + </table> +%endif \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/requests/view_request.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/view_request.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,20 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div> + %for index, rd in enumerate(request_details): + <div class="form-row"> + <label>${rd['label']}</label> + ##<i>${rd['helptext']}</i> + ${rd['value']} + </div> + <div style="clear: both"></div> + %endfor + </div> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/samples/change_state.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/samples/change_state.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,30 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif +<div class="toolForm"> + <div class="toolFormTitle">${title}</div> + <div class="toolFormBody"> + <form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id_list=sample_id_list)}" method="post" > + %for w in widgets: + <div class="form-row"> + <label> + ${w[0]} + </label> + ${w[1].get_html()} + %if w[0] == 'Comments': + <div class="toolParamHelp" style="clear: both;"> + Optional + </div> + %endif + </div> + %endfor + <div class="form-row"> + <input type="submit" name="add_event" value="Save"/> + </div> + </form> + </div> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/samples/edit_sample.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/samples/edit_sample.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,83 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Edit sample named: ${values.content['Name']}</div> + <div class="toolFormBody"> + <form name="sample" action="${h.url_for( controller='sample', action='do', save_changes=True, sample_id=sample.id )}" method="post" > + <div class="form-row"> + <label> + Library: + </label> + <select name="library_id"> + %for library in libraries: + <option value="${library.id}">${library.name}</option> + %endfor + </select> + </div> + %for i, field in enumerate(form.fields): + <div class="form-row"> + <label>${field['label']}</label> + %if field['type'] == 'TextField': + <input type="text" name="${field['label']}" value="${values.content[field['label']]}" size="40"/> + %elif field['type'] == 'TextArea': + <textarea name="${field['label']}" rows="3" cols="35">${values.content[field['label']]}</textarea> + %elif field['type'] == 'CheckBox': + %if values.content[field['label']] == "true": + <input type="checkbox" name="${field['label']}" value="true" checked> + %else: + <input type="checkbox" name="${field['label']}" value="true"> + %endif + %elif field['type'] == 'SelectBox': + <select name="${field['label']}"> + %for ft in field['selectlist']: + %if ft == values.content[field['label']]: + <option value="${ft}" selected>${ft}</option> + %else: + <option value="${ft}">${ft}</option> + %endif + %endfor + </select> + %endif + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="new" value="submitted" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="create_library_button" value="Save"/> + </div> + </form> + </div> +</div> +<div class="toolForm"> + <div class="toolFormBody"> + <form name="event" action="${h.url_for( controller='admin', action='event', new=True, sample_id=sample.id)}" method="post" > + <div class="form-row"> + <label> + Change sample state to: + </label> + <select name="state_id"> + %for state in states: + <option value="${state.id}">${state.name}</option> + %endfor + </select> + </div> + <div class="form-row"> + <input type="submit" name="add_event" value="Save"/> + </div> + </form> + </div> +</div> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/samples/events.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/samples/events.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,33 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="title()">Events for Sample ${sample_name}</%def> + +<h2>Events for Sample "${sample_name}" of Request: ${request}</h2> +<h3>User: ${user.email}</h3> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + + +<table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Description</th> + <th>Last Update</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for state, desc, updated, comments in events_list: + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td><b><a>${state}</a></b></td> + <td><a>${desc}</a></td> + <td><a>${updated}</a></td> + <td><a>${comments}</a></td> + </tr> + %endfor + </tbody> +</table> \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/admin/samples/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/samples/grid.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,203 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="title()">Browse Samples</%def> + +%if message: + <p> + <div class="${message_type}message transient-message">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + </script> +</%def> + +<%def name="stylesheets()"> + <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + <style> + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + </style> +</%def> + +<div class="grid-header"> + <h2>Samples associated with request: ${grid.request.name}</h2> + <h3>User: ${grid.user.email}</h3> +## %if len(query.all()): +## <span class="title">Filter:</span> +## %for i, filter in enumerate( grid.standard_filters ): +## %if i > 0: +## <span>|</span> +## %endif +## <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> +## %endfor +## %endif +</div> + +%if not len(query.all()): + There are no sample(s). +%else: +<form name="history_actions" action="${url()}" method="post" > + <table class="grid"> + <thead> + <tr> + <th></th> + %for column in grid.columns: + %if column.visible: + <% + href = "" + extra = "" + if column.sortable: + if sort_key == column.key: + if sort_order == "asc": + href = url( sort=( "-" + column.key ) ) + extra = "↓" + else: + href = url( sort=( column.key ) ) + extra = "↑" + else: + href = url( sort=column.key ) + %> + <th\ + %if column.ncells > 1: + colspan="${column.ncells}" + %endif + > + %if href: + <a href="${href}">${column.label}</a> + %else: + ${column.label} + %endif + <span>${extra}</span> + </th> + %endif + %endfor + <th></th> + </tr> + </thead> + <tbody> + %for i, item in enumerate( query ): + <tr \ + %if current_item == item: + class="current" \ + %endif + > + ## Item selection column + <td style="width: 1.5em;"> + <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> + </td> + ## Data columns + %for column in grid.columns: + %if column.visible: + <% + # Link + if column.link and column.link( item ): + href = url( **column.link( item ) ) + else: + href = None + # Value (coerced to list so we can loop) + value = column.get_value( trans, grid, item ) + if column.ncells == 1: + value = [ value ] + %> + %for cellnum, v in enumerate( value ): + <% + # Attach popup menu? + if column.attach_popup and cellnum == 0: + extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">▼</a>' % i + else: + extra = "" + %> + %if href: + <td><a href="${href}">${v}</a> ${extra}</td> + %else: + <td >${v}${extra}</td> + %endif + </td> + %endfor + %endif + %endfor + ## Actions column + <td> + <div popupmenu="grid-${i}-popup"> + %for operation in grid.operations: + %if operation.allowed( item ): + <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + %endfor + </tbody> + <tfoot> + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected requests: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + </tfoot> + </table> +</form> + +%endif diff -r 267db48a2371 -r b46f27137744 templates/admin/samples/view_sample.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/samples/view_sample.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,19 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Sample Details: '${sample_details[0]['value']}'</div> + %for index, rd in enumerate(sample_details): + <div class="form-row"> + <label>${rd['label']}</label> + ${rd['value']} + </div> + <div style="clear: both"></div> + %endfor + </div> +</div> diff -r 267db48a2371 -r b46f27137744 templates/base.mako --- a/templates/base.mako Thu Jul 09 15:49:26 2009 -0400 +++ b/templates/base.mako Fri Jul 10 11:37:28 2009 -0400 @@ -29,4 +29,33 @@ ## <![endif]--> <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> <script type="text/javascript" src="${h.url_for('/static/scripts/galaxy.base.js')}"></script> + + </%def> + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( ':file' ).each( function() { + var file_value = $( this )[0].value; + } ); + $( "#edit_form" ).submit(); + } + }); +}); \ No newline at end of file diff -r 267db48a2371 -r b46f27137744 templates/base_panels.mako --- a/templates/base_panels.mako Thu Jul 09 15:49:26 2009 -0400 +++ b/templates/base_panels.mako Fri Jul 10 11:37:28 2009 -0400 @@ -153,6 +153,8 @@ ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))} + + ${tab( "requests", "Requests", h.url_for( controller='requests', action='index' ), visible = (trans.user and trans.request_types)) } %if app.config.get_bool( 'enable_tracks', False ): <span class="tab"> diff -r 267db48a2371 -r b46f27137744 templates/requests/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/requests/grid.mako Fri Jul 10 11:37:28 2009 -0400 @@ -0,0 +1,210 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="title()">Browse Samples</%def> + +%if message: + <p> + <div class="${message_type}message transient-message">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + </script> +</%def> + +<%def name="stylesheets()">

1 0

[hg] galaxy 2474: Fixed another bug in saving special characters...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/615a0bcf870b changeset: 2474:615a0bcf870b user: rc date: Fri Jul 10 15:24:01 2009 -0400 description: Fixed another bug in saving special characters in forms 1 file(s) affected in this change: lib/galaxy/web/controllers/forms.py diffs (25 lines): diff -r f7bdfd409b7d -r 615a0bcf870b lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Fri Jul 10 14:50:17 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Fri Jul 10 15:24:01 2009 -0400 @@ -152,7 +152,7 @@ def __get_field(self, params, index): name = util.restore_text( params.get( 'field_name_%i' % index, None ) ) helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) ) - required = util.restore_text( params.get( 'field_required_%i' % index, False ) ) + required = params.get( 'field_required_%i' % index, False ) field_type = util.restore_text( params.get( 'field_type_%i' % index, None ) ) if field_type == 'SelectField': selectlist = self.__get_selectbox_options(params, index) @@ -172,10 +172,10 @@ ctr=0 sb_options = [] while True: - option = util.restore_text( params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) ) + option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) ctr = ctr+1 if option: - sb_options.append(option) + sb_options.append(util.restore_text(option)) else: return sb_options def __get_saved_form(self, fd):

1 0

[hg] galaxy 2470: Some history sharing cleanup and a fix for job...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/267db48a2371 changeset: 2470:267db48a2371 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Jul 09 15:49:26 2009 -0400 description: Some history sharing cleanup and a fix for job error reports. 5 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/history.py templates/history/list_shared.mako templates/history/share.mako test/functional/test_history_functions.py diffs (364 lines): diff -r 073c9a0b2467 -r 267db48a2371 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Jul 08 17:01:49 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Jul 09 15:49:26 2009 -0400 @@ -17,7 +17,7 @@ ------------------------ This error report was sent from the Galaxy instance hosted on the server -"${remote_hostname}" +"${host}" ----------------------------------------------------------------------------- This is in reference to output dataset ${dataset_id}. ----------------------------------------------------------------------------- @@ -65,10 +65,10 @@ dataset = model.HistoryDatasetAssociation.get( id ) job = dataset.creating_job_associations[0].job # Get the name of the server hosting the Galaxy instance from which this report originated - remote_hostname = trans.request.remote_hostname + host = trans.request.host # Build the email message msg = MIMEText( string.Template( error_report_template ) - .safe_substitute( remote_hostname=remote_hostname, + .safe_substitute( host=host, dataset_id=dataset.id, email=email, message=message, diff -r 073c9a0b2467 -r 267db48a2371 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Wed Jul 08 17:01:49 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Jul 09 15:49:26 2009 -0400 @@ -310,8 +310,9 @@ email=email, send_to_err=send_to_err ) if params.get( 'share_button', False ): - can_change, cannot_change, no_change_needed, send_to_err = \ - self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err ) + # The user has not yet made a choice about how to share, so dictionaries will be built for display + can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \ + self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err, unique=True ) if can_change or cannot_change: return trans.fill_template( "/history/share.mako", histories=histories, @@ -319,7 +320,7 @@ send_to_err=send_to_err, can_change=can_change, cannot_change=cannot_change, - no_change_needed=no_change_needed ) + no_change_needed=unique_no_change_needed ) if no_change_needed: return self._share_histories( trans, user, send_to_err, histories=no_change_needed ) elif not send_to_err: @@ -335,7 +336,8 @@ user = trans.get_user() histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email ) send_to_err = '' - can_change, cannot_change, no_change_needed, send_to_err = \ + # The user has made a choice, so dictionaries will be built for sharing + can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \ self._populate_restricted( trans, user, histories, send_to_users, action, send_to_err ) # Now that we've populated the can_change, cannot_change, and no_change_needed dictionaries, # we'll populate the histories_for_sharing dictionary from each of them. @@ -408,13 +410,13 @@ send_to_err += "%s is not a valid Galaxy user. " % email_address return histories, send_to_users, send_to_err def _populate( self, trans, histories_for_sharing, other, send_to_err ): - # this method will populate the histories_for_sharing dictionary with the users and + # This method will populate the histories_for_sharing dictionary with the users and # histories in other, eliminating histories that have already been shared with the # associated user. No security checking on datasets is performed. # If not empty, the histories_for_sharing dictionary looks like: # { userA: [ historyX, historyY ], userB: [ historyY ] } # other looks like: - # ## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } + # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } for send_to_user, history_dict in other.items(): for history in history_dict: # Make sure the current history has not already been shared with the current send_to_user @@ -430,20 +432,22 @@ elif history not in histories_for_sharing[ send_to_user ]: histories_for_sharing[ send_to_user ].append( history ) return histories_for_sharing, send_to_err - def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err ): + def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err, unique=False ): # The user may be attempting to share histories whose datasets cannot all be accessed by other users. # If this is the case, the user sharing the histories can: # 1) action=='public': choose to make the datasets public if he is permitted to do so # 2) action=='private': automatically create a new "sharing role" allowing protected # datasets to be accessed only by the desired users - # 3) action=='share_anyway': share only what can be shared when no permissions are changed - # 4) action=='no_share': Do not share anything - # In addition, the user may be sharing a history with a user with which the history was already shared - # and it will not be shared twice. - # This method will populate the can_change, cannot_change and no_change_needed dictionaries. + # This method will populate the can_change, cannot_change and no_change_needed dictionaries, which + # are used for either displaying to the user, letting them make 1 of the choices above, or sharing + # after the user has made a choice. They will be used for display if 'unique' is True, and will look + # like: {historyX : [hda, hda], historyY : [hda] } + # For sharing, they will look like: + # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } can_change = {} cannot_change = {} no_change_needed = {} + unique_no_change_needed = {} for history in histories: for send_to_user in send_to_users: # Make sure the current history has not already been shared with the current send_to_user @@ -456,7 +460,15 @@ # Only deal with datasets that have not been purged for hda in history.activatable_datasets: if trans.app.security_agent.dataset_is_public( hda.dataset ): - # Build the dict that will show the user what doesn't need to be changed + # The no_change_needed dictionary is a special case. If both of can_change + # and cannot_change are empty, no_change_needed will used for sharing. Otherwise + # unique_no_change_needed will be used for displaying, so we need to populate both. + # Build the dictionaries for display, containing unique histories only + if history not in unique_no_change_needed: + unique_no_change_needed[ history ] = [ hda ] + else: + unique_no_change_needed[ history ].append( hda ) + # Build the dictionaries for sharing if send_to_user not in no_change_needed: no_change_needed[ send_to_user ] = {} if history not in no_change_needed[ send_to_user ]: @@ -473,28 +485,40 @@ # The current user has authority to change permissions on the current dataset because # they have permission to manage permissions on the dataset and the dataset is not associated # with a library. - if send_to_user not in can_change: - # Build the set of histories / datasets on which the current user has authority - # to "manage permissions". - can_change[ send_to_user ] = {} - if history not in can_change[ send_to_user ]: - can_change[ send_to_user ][ history ] = [ hda ] + if unique: + # Build the dictionaries for display, containing unique histories only + if history not in can_change: + can_change[ history ] = [ hda ] + else: + can_change[ history ].append( hda ) else: - can_change[ send_to_user ][ history ].append( hda ) + # Build the dictionaries for sharing + if send_to_user not in can_change: + can_change[ send_to_user ] = {} + if history not in can_change[ send_to_user ]: + can_change[ send_to_user ][ history ] = [ hda ] + else: + can_change[ send_to_user ][ history ].append( hda ) else: if action in [ "private", "public" ]: - # Don't change stuff that the user doesn't have permission to change + # The user has made a choice, so 'unique' doesn't apply. Don't change stuff + # that the user doesn't have permission to change continue - #elif send_to_user not in cannot_change: - if send_to_user not in cannot_change: - # Build the set of histories / datasets on which the current user does - # not have authority to "manage permissions". - cannot_change[ send_to_user ] = {} - if history not in cannot_change[ send_to_user ]: - cannot_change[ send_to_user ][ history ] = [ hda ] + if unique: + # Build the dictionaries for display, containing unique histories only + if history not in cannot_change: + cannot_change[ history ] = [ hda ] + else: + cannot_change[ history ].append( hda ) else: - cannot_change[ send_to_user ][ history ].append( hda ) - return can_change, cannot_change, no_change_needed, send_to_err + # Build the dictionaries for sharing + if send_to_user not in cannot_change: + cannot_change[ send_to_user ] = {} + if history not in cannot_change[ send_to_user ]: + cannot_change[ send_to_user ][ history ] = [ hda ] + else: + cannot_change[ send_to_user ][ history ].append( hda ) + return can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err def _share_histories( self, trans, user, send_to_err, histories={} ): # histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] } msg = "" @@ -605,6 +629,7 @@ if clone_choice == 'activatable': new_history = history.copy( name=name, target_user=user, activatable=True ) elif clone_choice == 'active': + name += " (active items only)" new_history = history.copy( name=name, target_user=user ) # Render the list view return trans.show_ok_message( 'Clone with name "%s" is now included in your list of stored histories.' % new_history.name ) diff -r 073c9a0b2467 -r 267db48a2371 templates/history/list_shared.mako --- a/templates/history/list_shared.mako Wed Jul 08 17:01:49 2009 -0400 +++ b/templates/history/list_shared.mako Thu Jul 09 15:49:26 2009 -0400 @@ -18,7 +18,7 @@ ${history.name} <a id="shared-${i}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ), clone_choice='activatable' )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ) )}">Clone</a> </div> </td> <td>${history.user.email}</td> diff -r 073c9a0b2467 -r 267db48a2371 templates/history/share.mako --- a/templates/history/share.mako Wed Jul 08 17:01:49 2009 -0400 +++ b/templates/history/share.mako Thu Jul 09 15:49:26 2009 -0400 @@ -64,35 +64,14 @@ <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> %endfor %if no_change_needed: + ## no_change_needed looks like: {historyX : [hda, hda], historyY : [hda] } <div style="clear: both"></div> <div class="form-row"> <div class="donemessage"> The following datasets can be shared with ${email} with no changes </div> - </div> - ## no_change_needed looks like: - ## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } - <% - # TODO: move generation of these unique dictionaries to the history controller - # Build the list of unique histories and datasets - unique_stuff = {} - %> - %for user, history_dict in no_change_needed.items(): - %for history, hdas in history_dict.items(): - <% - if history in unique_stuff: - for hda in hdas: - if hda not in unique_stuff[ history ]: - unique_stuff[ history ].append( hda ) - else: - unique_stuff[ history ] = [] - for hda in hdas: - if hda not in unique_stuff[ history ]: - unique_stuff[ history ].append( hda ) - %> - %endfor - %endfor - %for history, hdas in unique_stuff.items(): + </div> + %for history, hdas in no_change_needed.items(): <div class="form-row"> <label>History</label> ${history.name} @@ -104,40 +83,22 @@ %for hda in hdas: <div class="form-row"> ${hda.name} + %if hda.deleted: + (deleted) + %endif </div> %endfor %endfor %endif %if can_change: + ## can_change looks like: {historyX : [hda, hda], historyY : [hda] } <div style="clear: both"></div> <div class="form-row"> <div class="warningmessage"> The following datasets can be shared with ${email} by updating their permissions </div> </div> - ## can_change looks like: - ## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } - <% - # TODO: move generation of these unique dictionaries to the history controller - # Build the list of unique histories and datasets - unique_stuff = {} - %> - %for user, history_dict in can_change.items(): - %for history, hdas in history_dict.items(): - <% - if history in unique_stuff: - for hda in hdas: - if hda not in unique_stuff[ history ]: - unique_stuff[ history ].append( hda ) - else: - unique_stuff[ history ] = [] - for hda in hdas: - if hda not in unique_stuff[ history ]: - unique_stuff[ history ].append( hda ) - %> - %endfor - %endfor - %for history, hdas in unique_stuff.items(): + %for history, hdas in can_change.items(): <div class="form-row"> <label>History</label> ${history.name} @@ -149,11 +110,15 @@ %for hda in hdas: <div class="form-row"> ${hda.name} + %if hda.deleted: + (deleted) + %endif </div> %endfor %endfor %endif %if cannot_change: + ## cannot_change looks like: {historyX : [hda, hda], historyY : [hda] } <div style="clear: both"></div> <div class="form-row"> <div class="errormessage"> @@ -161,29 +126,7 @@ change the permissions on them </div> </div> - ## cannot_change looks like: - ## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } - <% - # TODO: move generation of these unique dictionaries to the history controller - # Build the list of unique histories and datasets - unique_stuff = {} - %> - %for user, history_dict in can_change.items(): - %for history, hdas in history_dict.items(): - <% - if history in unique_stuff: - for hda in hdas: - if hda not in unique_stuff[ history ]: - unique_stuff[ history ].append( hda ) - else: - unique_stuff[ history ] = [] - for hda in hdas: - if hda not in unique_stuff[ history ]: - unique_stuff[ history ].append( hda ) - %> - %endfor - %endfor - %for history, hdas in unique_stuff.items(): + %for history, hdas in cannot_change.items(): <div class="form-row"> <label>History</label> ${history.name} @@ -195,10 +138,17 @@ %for hda in hdas: <div class="form-row"> ${hda.name} + %if hda.deleted: + (deleted) + %endif </div> %endfor %endfor %endif + <div class="toolFormTitle"></div> + <div class="form-row"> + Deleted items can be eliminated by the users with which you are sharing the history. + </div> <div class="form-row"> <label>How would you like to proceed?</label> </div> diff -r 073c9a0b2467 -r 267db48a2371 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Wed Jul 08 17:01:49 2009 -0400 +++ b/test/functional/test_history_functions.py Thu Jul 09 15:49:26 2009 -0400 @@ -253,7 +253,7 @@ # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( check_str="Clone of '%s'" % history3.name ) # Switch to the cloned history to make sure activatable datasets were cloned - self.switch_history( id=self.security.encode_id( history3_clone3.id ), name=history3_clone3.name ) + self.switch_history( id=self.security.encode_id( history3_clone3.id ) ) # Make sure the deleted datasets are NOT included in the cloned history try: self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True )

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